Mercurial > repos > chemteam > gmx_fep
changeset 0:19d1d4c30402 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
| author | chemteam |
|---|---|
| date | Mon, 11 Nov 2019 13:20:39 -0500 |
| parents | |
| children | 453311042f29 |
| files | alchemical_run/gmx_fep.sh alchemical_run/gmx_fep.xml alchemical_run/test-data/Input_files.tar alchemical_run/test-data/Report.txt alchemical_run/test-data/TI_FEP_data_output.tar alchemical_run/test-data/morph.gro alchemical_run/test-data/morph.top |
| diffstat | 7 files changed, 9018 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alchemical_run/gmx_fep.sh Mon Nov 11 13:20:39 2019 -0500 @@ -0,0 +1,114 @@ +#!/bin/bash + +# _________ read inputs from the galaxy wrapper and define some variables ____________ + +lam=$1 +iter=$((lam+1)) + +mkdir MDP +mkdir data +mkdir traj + +FREE_ENERGY=`pwd` +MDP=$FREE_ENERGY/MDP + + +for i in `seq 0 $lam` + do + cp em_steep.mdp em_steep_$i.mdp + sed -i "s/%L%/$i/" em_steep_$i.mdp + cp nvt.mdp nvt_$i.mdp + sed -i "s/%L%/$i/" nvt_$i.mdp + cp npt.mdp npt_$i.mdp + sed -i "s/%L%/$i/" npt_$i.mdp + cp md.mdp md_$i.mdp + sed -i "s/%L%/$i/" md_$i.mdp + done +mv *.mdp $MDP + +for (( i=0; i<$iter; i++ )) +do + LAMBDA=$i + + # A new directory will be created for each value of lambda + + mkdir Lambda_$LAMBDA + cd Lambda_$LAMBDA + +# _______ ENERGY MINIMIZATION STEEP _______ + + echo "Starting minimization for lambda = $LAMBDA..." + + mkdir EM + cd EM + + # Iterative calls to grompp and mdrun to run the simulations + + gmx grompp -f $MDP/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/morph.gro -p $FREE_ENERGY/morph.top -o min$LAMBDA.tpr + + gmx mdrun -deffnm min$LAMBDA + + sleep 10 + + +# _______ NVT EQUILIBRATION _______ + + echo "Starting constant volume equilibration..." + + cd ../ + mkdir NVT + cd NVT + + gmx grompp -f $MDP/nvt_$LAMBDA.mdp -c ../EM/min$LAMBDA.gro -p $FREE_ENERGY/morph.top -o nvt$LAMBDA.tpr + + gmx mdrun -deffnm nvt$LAMBDA + + echo "Constant volume equilibration complete." + + sleep 10 + +# _______ NPT EQUILIBRATION _______ + + echo "Starting constant pressure equilibration..." + + cd ../ + mkdir NPT + cd NPT + + gmx grompp -f $MDP/npt_$LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p $FREE_ENERGY/morph.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr + + gmx mdrun -deffnm npt$LAMBDA + + echo "Constant pressure equilibration complete." + + sleep 10 + +# ________ PRODUCTION MD ___________ + + echo "Starting production MD simulation..." + + cd ../ + mkdir Production_MD + cd Production_MD + + gmx grompp -f $MDP/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p $FREE_ENERGY/morph.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr + + gmx mdrun -deffnm md$LAMBDA + + echo "Production MD complete." + + # End + echo "Ending. Job completed for lambda = $LAMBDA" + + cd $FREE_ENERGY +done + +cp Lambda_*/Production_MD/*.xvg data/ +tar cf data.tar data/ + +cp Lambda_*/Production_MD/*.trr traj/ +tar cf traj.tar traj/ + +exit; + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alchemical_run/gmx_fep.xml Mon Nov 11 13:20:39 2019 -0500 @@ -0,0 +1,552 @@ +<tool id="gmx_fep" name="Alchemical Run" version="2019.1"> + <description>Alchemical free energy simulations using gromacs</description> + <requirements> + <requirement type="package" version="2019.1">gromacs</requirement> + </requirements> +<command detect_errors="exit_code"><![CDATA[ + ln -s '$em_steep' ./em_steep.mdp && + ln -s '$nvt' ./nvt.mdp && + ln -s '$npt' ./npt.mdp && + ln -s '$md' ./md.mdp && + + ln -s '$groin' ./morph.gro && + ln -s '$topin' ./morph.top && + + #if $input_fep == 'perform': + bash '$__tool_directory__/gmx_fep.sh' '$path.lambda' &>> '$report' + #end if + #if $input_fep == 'generate': + mkdir -p input_files && + cp '$__tool_directory__/gmx_fep.sh' input_files/ && + cp ./em_steep.mdp input_files/ && + cp ./nvt.mdp input_files/ && + cp ./npt.mdp input_files/ && + cp ./md.mdp input_files/ && + cp ./morph.gro input_files/ && + cp ./morph.top input_files/ && + tar cf input_files.tar input_files/ + #end if + ]]></command> + <configfiles> + <configfile name="em_steep"> +integrator = steep +nsteps = $minstep +emtol = 100 +emstep = 0.01 +niter = 20 +nbfgscorr = 10 +nstlog = 1 +nstenergy = 1 +cutoff-scheme = verlet +nstlist = 10 +ns_type = grid +pbc = xyz +rlist = 1.2 +coulombtype = PME +rcoulomb = 1.2 +vdwtype = cutoff +vdw-modifier = potential-switch +rvdw-switch = 1.0 +rvdw = 1.2 +DispCorr = EnerPres +fourierspacing = 0.12 +pme_order = 6 +ewald_rtol = 1e-06 +epsilon_surface = 0 +tcoupl = no +pcoupl = no +ld-seed = -1 +gen-seed = $seed +free_energy = no +delta_lambda = 0 +calc_lambda_neighbors = 1 +init-lambda-state = %L% + +#if $path.select_path == "global": +fep-lambdas = $path.fep +#end if + +#if $path.select_path in ["default1", "default2"]: +coul-lambdas = $path.coul +vdw-lambdas = $path.vdw +bonded-lambdas = $path.bonded +#end if + +sc-alpha = 0.5 +sc-coul = no +sc-power = 1 +sc-sigma = 0.3 +nstdhdl = 10 + +gen_vel = no +constraints = none + </configfile> + <configfile name="nvt"> +integrator = sd +tinit = 0 +dt = $dt +nsteps = $nvtstep +nstcomm = 100 +nstxout = 500 +nstvout = 500 +nstfout = 0 +nstlog = 500 +nstenergy = 500 +nstxout-compressed = 0 +cutoff-scheme = verlet +nstlist = 20 +ns_type = grid +pbc = xyz +rlist = 1.2 +coulombtype = PME +rcoulomb = 1.2 +vdwtype = cutoff +vdw-modifier = potential-switch +rvdw-switch = 1.0 +rvdw = 1.2 +DispCorr = EnerPres +fourierspacing = 0.12 +pme_order = 6 +ewald_rtol = 1e-06 +epsilon_surface = 0 +tc_grps = system +tau_t = 1.0 +ref_t = $temperature +Pcoupl = No +tau_p = 0.5 +compressibility = 4.5e-05 +ref_p = $pressure +ld-seed = -1 +gen-seed = $seed +free_energy = no +delta_lambda = 0 +calc_lambda_neighbors = 1 +init-lambda-state = %L% + +#if $path.select_path == "global": +fep-lambdas = $path.fep +#end if + +#if $path.select_path in ["default1", "default2"]: +coul-lambdas = $path.coul +vdw-lambdas = $path.vdw +bonded-lambdas = $path.bonded +#end if + +sc-alpha = 0.5 +sc-coul = no +sc-power = 1 +sc-sigma = 0.3 +nstdhdl = 10 +gen_vel = yes +gen_temp = 300 + +#if $constraints.cons == "no": +constraints = none +#end if + +#if $constraints.cons == "yes": +constraints = $constraints.cons_type +constraint-algorithm = lincs +lincs-order = $constraints.lincs_order +lincs-iter = $constraints.lincs_iter +lincs-warnangle = $constraints.lincs_warnangle +#end if + </configfile> + <configfile name="npt"> +integrator = sd +tinit = 0 +dt = $dt +nsteps = $nptstep +nstcomm = 100 +nstxout = 500 +nstvout = 500 +nstfout = 0 +nstlog = 500 +nstenergy = 500 +nstxout-compressed = 0 +cutoff-scheme = verlet +nstlist = 20 +ns_type = grid +pbc = xyz +rlist = 1.2 +coulombtype = PME +rcoulomb = 1.2 +vdwtype = cutoff +vdw-modifier = potential-switch +rvdw-switch = 1.0 +rvdw = 1.2 +DispCorr = EnerPres +fourierspacing = 0.12 +pme_order = 6 +ewald_rtol = 1e-06 +epsilon_surface = 0 +tc_grps = System +tau_t = 1.0 +ref_t = $temperature +Pcoupl = Berendsen +tau_p = 0.5 +compressibility = 4.5e-05 +ref_p = $pressure +ld-seed = -1 +gen-seed = $seed +free_energy = no +delta_lambda = 0 +calc_lambda_neighbors = 1 +init-lambda-state = %L% + +#if $path.select_path == "global": +fep-lambdas = $path.fep +#end if + +#if $path.select_path in ["default1", "default2"]: +coul-lambdas = $path.coul +vdw-lambdas = $path.vdw +bonded-lambdas = $path.bonded +#end if + +; Options for the decoupling +sc-alpha = 0.5 +sc-coul = no +sc-power = 1 +sc-sigma = 0.3 +nstdhdl = 10 +gen_vel = no + +#if $constraints.cons == "no": +constraints = none +#end if + +#if $constraints.cons == "yes": +constraints = $constraints.cons_type +constraint-algorithm = lincs +lincs-order = $constraints.lincs_order +lincs-iter = $constraints.lincs_iter +lincs-warnangle = $constraints.lincs_warnangle +#end if + </configfile> + <configfile name="md"> +integrator = sd +bd-fric = 0 +dt = $dt +nsteps = $mdstep +nstcomm = 100 + +nstxout = 10000 +nstvout = 0 +nstfout = 0 +nstlog = 10000 +nstenergy = 10000 +nstxout-compressed = 0 + +tcoupl = no +nsttcouple = 10 +tc_grps = System +tau_t = 1.0 +ref_t = $temperature + +#if $constraints.cons == "no": +constraints = none +#end if + +#if $constraints.cons == "yes": +constraints = $constraints.cons_type +constraint-algorithm = lincs +lincs-order = $constraints.lincs_order +lincs-iter = $constraints.lincs_iter +lincs-warnangle = $constraints.lincs_warnangle +#end if + +comm-mode = Linear + +cutoff-scheme = Verlet +nstlist = 10 +ns_type = grid +pbc = xyz +rlist = 0.8 + +coulombtype = PME +coulomb-modifier = none +rcoulomb = 0.8 +fourierspacing = 0.10 +pme_order = 4 +ewald_rtol = 1.0E-5 + +vdwtype = cut-off +vdw-modifier = none +rvdw = 0.8 +DispCorr = AllEnerPres + +pcoupl = Parrinello-Rahman +pcoupltype = isotropic +tau_p = 2 +compressibility = 4.5e-5 +ref_p = $pressure +refcoord-scaling = com + +gen-vel = no +continuation = yes + +ld-seed = -1 +gen-seed = $seed + +free-energy = yes +delta-lambda = 0 ; do not use slow growth method +init-lambda-state = %L% + +#if $path.select_path == "global": +fep-lambdas = $path.fep +#end if + +#if $path.select_path in ["default1", "default2"]: +coul-lambdas = $path.coul +vdw-lambdas = $path.vdw +bonded-lambdas = $path.bonded +#end if + +nstdhdl = 10 +nstcalcenergy = 10 +calc-lambda-neighbors = -1 + +#if $feoptions.feop == "default": +sc-alpha = 0.5 +sc-coul = no +sc-power = 1 +sc-r-power = 6 +sc-sigma = 0.3 +couple-lambda0 = vdw-q +couple-lambda1 = none +couple-intramol = no +#end if + +#if $feoptions.feop == "modify": +sc-alpha = $feoptions.scalpha +sc-coul = $feoptions.sccoul +sc-power = $feoptions.scpower +sc-r-power = $feoptions.scrpower +sc-sigma = $feoptions.scsigma +couple-lambda0 = $feoptions.couplelambda0 +couple-lambda1 = $feoptions.couplelambda1 +couple-intramol = $feoptions.coupleintramol +#end if + +dhdl-derivatives = yes +dhdl-print-energy = no +separate-dhdl-file = yes +dh_hist_size = 0 +dh_hist_spacing = 0.1 + + </configfile> + </configfiles> + <inputs> + <param format="gro" name="groin" type="data" label="Structure (GRO) file" help="GRO input file with the merged structure."/> + <param format="top" name="topin" type="data" label="Topology (TOP) file" help="TOP input file with the merged structure."/> + <param name="minstep" type="integer" value="10000" label="Minimization steps" help="Number of steps for each free energy window."/> + <param name="nvtstep" type="integer" value="500000" label="NVT equilibration steps" help="Number of MD steps for NVT equilibration for each free energy window."/> + <param name="nptstep" type="integer" value="500000" label="NPT equilibration steps" help="Number of MD steps for NPT equilibration for each free energy window."/> + <param name="mdstep" type="integer" value="1000000" label="MD (production) steps" help="Number of MD steps for production runs of each free energy window."/> + <param name="seed" type="integer" value="19880924" label="Seed" help="Seed to initialize random generator for random velocities."/> + <param name="dt" type="float" value="0.001" label="Time step (ps)" help="Time step for integration."/> + <conditional name="constraints"> + <param name="cons" type="select" label="Apply constraints to the ligands?" help="Constraints may be required to keep the ligands with alchemical states in the active site."> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="cons_type" type="select" label="Constraints type" help="Convert all bonds to constraints, or only those containing hydrogen atoms"> + <option value="h-bonds" selected="true">H-bonds</option> + <option value="all-bonds">All bonds</option> + </param> + <param name="lincs_order" type="integer" value="4" label="LINCS order" help="Accuracy of LINCS algorithm. For normal MD simulations an order of 4 usually suffices, 6 is needed for large time-steps with virtual sites or BD."/> + <param name="lincs_iter" type="integer" value="1" label="LINCS iterations" help="Number of iterations to correct for rotational lengthening in LINCS. For normal runs a single step is sufficient."/> + <param name="lincs_warnangle" type="integer" value="30" label="LINCS maximum angle" help="Maximum angle that a bond can rotate before LINCS will complain / [deg]"/> + </when> + </conditional> + <conditional name="path"> + <param name="select_path" type="select" label="Select the FEP path"> + <option value="global">Use global lambda scaling</option> + <option value="default1">Default option 1 (change a larger ligand to a smaller ligand)</option> + <option value="default2">Default option 2 (change a smaller ligand to a larger ligand)</option> + </param> + <when value="global"> + <param name="lambda" type="text" value="2" label="Number of free energy windows"/> + <param name="fep" type="text" value="0.00 0.50 1.00" label="FEP Lambdas" help="Global scaling - values must be between 0 and 1."/> + </when> + <when value="default1"> + <param name="lambda" type="text" value="40" label="Number of free energy windows"/> + <param name="coul" type="text" value="0.00 0.11 0.22 0.33 0.44 0.56 0.67 0.78 0.89 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.000 1.00" label="Coulomb Lambdas (scaling electrostatics)" help="Values must be between 0 and 1."/> + <param name="vdw" type="text" value="0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00" label="Van der Waals Lambdas (scaling vdw interactions)" help="Values must be between 0 and 1."/> + <param name="bonded" type="text" value="0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00" label="Bonded Lambdas (scaling torsion)" help="Values must be between 0 and 1."/> + </when> + <when value="default2"> + <param name="lambda" type="text" value="40" label="Number of free energy windows"/> + <param name="coul" type="text" value="0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.000 0.00 0.11 0.22 0.33 0.44 0.56 0.67 0.78 0.89 1.00 " label="Coulomb Lambdas (scaling electrostatics)" help="Values must be between 0 and 1."/> + <param name="vdw" type="text" value="0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00" label="Van der Waals Lambdas (scaling vdw interactions)" help="Values must be between 0 and 1."/> + <param name="bonded" type="text" value="0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00" label="Bonded Lambdas (scaling torsion)" help="Values must be between 0 and 1."/> + </when> + </conditional> + <conditional name="feoptions"> + <param name="feop" type="select" label="Free energy variables"> + <option value="default">Use default options</option> + <option value="modify">Modify default options</option> + </param> + <when value="default"/> + <when value="modify"> + <param name="scalpha" type="float" value="0.5" label="The soft-core alpha parameter (sc-alpha)" /> + <param name="scrpower" type="integer" value="6" label="The power of the radial term in the soft-core equation (sc-r-power)" /> + <param name="scpower" type="integer" value="1" label="The power for lambda in the soft-core function (sc-power)" /> + <param name="sccoul" type="text" value="no" label="Apply the soft-core free energy interaction transformation to the Columbic interaction of a molecule (sc-coul)? "/> + <param name="scsigma" type="float" value="0.3" label="The soft-core sigma" /> + <param name="couplelambda0" type="text" value="vdw-q" label="Interactions at lambda=0" help="options are vdw-q, vdw, q, or none"/> + <param name="couplelambda1" type="text" value="none" label="Interactions at lambda=1" help="options are vdw-q, vdw, q, or none"/> + <param name="coupleintramol" type="text" value="no" label="Turn off intra-molecular interactions?" /> + </when> + </conditional> + <param name="temperature" type="float" value="300.0" label="Temperature /K" /> + <param name="pressure" type="float" value="1.0" label="Pressure /bar" /> + <param name="input_fep" type="select" label="Perform simulation or only generate input files?"> + <option value="perform">Perform simulation</option> + <option value="generate">Only generate input files</option> + </param> + </inputs> + <outputs> + <data name="fepinpout" format="tar" from_work_dir="input_files.tar" label="Input files"> + <filter>input_fep == 'generate'</filter> + </data> + <data name="dataout" format="tar" from_work_dir="data.tar" label="TI/FEP data output"> + <filter>input_fep == 'perform'</filter> + </data> + <data name="trajout" format="tar" from_work_dir="traj.tar" label="Trajectories output"> + <filter>input_fep == 'perform'</filter> + </data> + <data name="report" format="txt" label="Report"> + <filter>input_fep == 'perform'</filter> + </data> + </outputs> + <tests> + <test> + <param name="groin" value="morph.gro" ftype="gro"/> + <param name="topin" value="morph.top" ftype="top"/> + <param name="minstep" value="10"/> + <param name="nvtstep" value="50"/> + <param name="nptstep" value="50"/> + <param name="mdstep" value="100"/> + <param name="seed" value="19880924"/> + <param name="cons" value="no"/> + <param name="dt" value="0.001"/> + <param name="path" value="global"/> + <param name="lambda" value="2"/> + <param name="fep" value="0.00 0.50 1.00"/> + <param name="temperature" value="300.0"/> + <param name="fepop" value="default"/> + <param name="input_fep" value="perform"/> + <param name="pressure" value="1.0"/> + <output name="dataout" file="TI_FEP_data_output.tar" compare="sim_size"/> + </test> + <test> + <param name="groin" value="morph.gro" ftype="gro"/> + <param name="topin" value="morph.top" ftype="top"/> + <param name="minstep" value="10000"/> + <param name="nvtstep" value="500000"/> + <param name="nptstep" value="500000"/> + <param name="mdstep" value="1000000"/> + <param name="seed" value="123546"/> + <param name="cons" value="yes"/> + <param name="cons_type" value="h-bonds"/> + <param name="lincs_order" value="4"/> + <param name="lincs_iter" value="1"/> + <param name="incs_warnangle" value="30"/> + <param name="dt" value="0.002"/> + <param name="path" value="default2"/> + <param name="lambda" value="40"/> + <param name="coul" value="0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.000 0.00 0.11 0.22 0.33 0.44 0.56 0.67 0.78 0.89 1.00"/> + <param name="vdw" value="0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00"/> + <param name="bonded" value="0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00"/> + <param name="temperature" value="300.0"/> + <param name="fepop" value="default"/> + <param name="input_fep" value="generate"/> + <param name="pressure" value="1.0"/> + <output name="fepinpout" file="Input_files.tar" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + + + - This tool can run the alchemical free energy calculations using GROMACS. + - For more details about alchemical free energy calculations see http://www.alchemistry.org/wiki/Main_Page + - For details about GROMACS simulations see http://manual.gromacs.org/documentation/2019-rc1/user-guide/mdp-options.html + +When you need to run the simulation outside Galaxy, you can generate and down load all the input files from this tool. + +1. Simply download the output "Input files". +2. Untar it using tar -xvf Galaxy3-\[Input_files\].tar +3. Run the bash script inside ./gmx_fep.sh {number of FEP windows} + - Give the number of FEP windows as an argument. + +This will generate input .MDP files and run all the steps for all the FEP windows iteratively. + + +_____ + + +.. class:: infomark + +**Rules of Thumb for Intermediate States (taken from alchemistry.org)** + + - These rules are not the end-all set and you should be familiar with why each one is suggested before just accepting them. + - Bonded terms can be modified/turned off linearly. This includes angle or bond force constants as well as unconstrained bond distances. + - Constrained bonds should not change length. There are free energy changes that cannot be ignored affiliated with this action. + - Maximize similarity between states by removing/decoupling as few atoms as possible. + - Do not open and close rings. This supersedes the previous rule. + - Statistical uncertainty between any neighboring states should be equal. Rather challenging to do, but it has been proven to have the lowest variance path if you can pull it off. + - Deleting or adding atoms should always be done with a soft core potential. + - Changes in parameters can be done linearly. + - All charge on atoms must be turned off prior to atomic repulsion. Otherwise you can get an infinite attractive potential and crash your simulation. + - Similarly for only changes in terms, it's generally more efficient to change electrostatic terms separate from Lennard-Jones terms. + - More states is better than fewer. Variance shrinks rapidly with number of states. You want the difference between intermediaries to be between 2-3 kBT + +Obviously you will be limited on CPU power. Fewer states also leads to more samples begin required from each state, so take this into account when deciding number of states as well. +However, for MBAR and TI, it can be shown that spreading samples across multiple states does not significantly affect the uncertainty, since for TI, each state contributes less to +the total uncertainty, and in MBAR, data contributes to the statistical precision of states with similar values of lambda. + +Shape of the variance does not significantly change with number of atoms, only magnitude. More intermediates will still be required for a large number of atoms to reduce statistical noise. +Charge should be maintained across all λ + +Simply having charged molecules is fine, but the net of the system should remain constant. If you must change the net charge, there are complicated ways to do so. + +Short prototype simulations are recommended. Even as short as 100 ps, the prototypes can provide rough magnitude of variance estimates, +although will likely under-predict the free energy as many configurations remain unsampled. + + +_____ + + +.. class:: infomark + +**Input** + + - .GRO input + - .TOP input + +_____ + + +.. class:: infomark + +**Output** + + - TI/FEP data + - TI/FEP trajectory + - Report + + ]]></help> + <citations> + <citation type="doi">10.1016/j.softx.2015.06.001</citation> + <citation type="bibtex">@misc{alchemistrywiki, title={Alchemistry.org}, url={http://www.alchemistry.org/wiki/Main_Page}, journal={AlchemistryWiki}} + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alchemical_run/test-data/Report.txt Mon Nov 11 13:20:39 2019 -0500 @@ -0,0 +1,1636 @@ +Starting minimization for lambda = 0... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/EM +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/em_steep_0.mdp -c /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o min0.tpr + +Setting the LD random seed to -127141127 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet +Number of degrees of freedom in T-Coupling group rest is 12987.00 +Estimate for the relative computational load of the PME mesh part: 0.21 + +GROMACS reminds you: "Wedged as we are between two eternities of idleness, there is no excuse for being idle now" (Anthony Burgess) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/EM +Command line: + gmx mdrun -deffnm min0 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file min0.tpr, VERSION 2019.1 (single precision) + +Using 1 MPI thread +Using 4 OpenMP threads + + +Steepest Descents: + Tolerance (Fmax) = 1.00000e+02 + Number of steps = 10 + +Energy minimization reached the maximum number of steps before the forces +reached the requested precision Fmax < 100. + +writing lowest energy coordinates. + +Steepest Descents did not converge to Fmax < 100 in 11 steps. +Potential Energy = -8.3125391e+04 +Maximum force = 2.1372287e+04 on atom 1 +Norm of force = 5.1859150e+02 + +GROMACS reminds you: "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." (Watson & Crick) + +Starting constant volume equilibration... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NVT +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/nvt_0.mdp -c ../EM/min0.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o nvt0.tpr + +Setting the LD random seed to -187712966 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Velocities were taken from a Maxwell distribution at 300 K +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 1 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Estimate for the relative computational load of the PME mesh part: 0.23 + +There was 1 note + +GROMACS reminds you: "Nada e organico, e tudo programado" (Pitty) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm +Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NVT +Command line: + gmx mdrun -deffnm nvt0 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file nvt0.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +50 steps, 0.1 ps. + +Writing final coordinates. + + Core t (s) Wall t (s) (%) + Time: 1.458 0.365 399.9 + (ns/day) (hour/ns) +Performance: 12.084 1.986 + +GROMACS reminds you: "I Quit My Job Blowing Leaves" (Beck) + +Constant volume equilibration complete. +Starting constant pressure equilibration... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NPT +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/npt_0.mdp -c ../NVT/nvt0.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NVT/nvt0.cpt -o npt0.tpr + +Setting the LD random seed to 2038796930 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 1 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Reading Coordinates, Velocities and Box size from old trajectory +Will read whole trajectory + Last frame -1 time 0.050 +Using frame at t = 0.05 ps +Starting time for run is 0 ps +Estimate for the relative computational load of the PME mesh part: 0.23 + +There was 1 note + +GROMACS reminds you: "Act like Prometheus would" (Gogol Bordello) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm +Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NPT +Command line: + gmx mdrun -deffnm npt0 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file npt0.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +50 steps, 0.1 ps. + +Writing final coordinates. + + Core t (s) Wall t (s) (%) + Time: 1.261 0.315 399.9 + (ns/day) (hour/ns) +Performance: 13.979 1.717 + +GROMACS reminds you: "I Was Born to Have Adventure" (F. Zappa) + +Constant pressure equilibration complete. +Starting production MD simulation... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/Production_MD +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_0.mdp -c ../NPT/npt0.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NPT/npt0.cpt -o md0.tpr + + +NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_0.mdp]: + With PME there is a minor soft core effect present at the cut-off, + proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on + energy conservation, but usually other effects dominate. With a common + sigma value of 0.34 nm the fraction of the particle-particle potential at + the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05. + +Setting the LD random seed to -1773803540 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 2 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Reading Coordinates, Velocities and Box size from old trajectory +Will read whole trajectory + Last frame -1 time 0.050 +Using frame at t = 0.05 ps +Starting time for run is 0 ps +Estimate for the relative computational load of the PME mesh part: 0.47 + +There were 2 notes + +GROMACS reminds you: "God is a DJ" (Faithless) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm +Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/Production_MD +Command line: + gmx mdrun -deffnm md0 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file md0.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 10 to 50, rlist from 0.8 to 0.86 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +2000 steps, 2.0 ps. + +Writing final coordinates. + + Core t (s) Wall t (s) (%) + Time: 27.033 6.758 400.0 + (ns/day) (hour/ns) +Performance: 25.581 0.938 + +GROMACS reminds you: "Don't You Wish You Never Met Her, Dirty Blue Gene?" (Captain Beefheart) + +Production MD complete. +Ending. Job completed for lambda = 0 +Starting minimization for lambda = 1... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/EM +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/em_steep_1.mdp -c /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o min1.tpr + +Setting the LD random seed to -1393309481 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet +Number of degrees of freedom in T-Coupling group rest is 12987.00 +Estimate for the relative computational load of the PME mesh part: 0.21 + +GROMACS reminds you: "Scientists think they are born with logic; God forbid they should study this discipline with a history of more than two and a half millennia." (Roald Hoffmann) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/EM +Command line: + gmx mdrun -deffnm min1 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file min1.tpr, VERSION 2019.1 (single precision) + +Using 1 MPI thread +Using 4 OpenMP threads + + +Steepest Descents: + Tolerance (Fmax) = 1.00000e+02 + Number of steps = 10 + +Energy minimization reached the maximum number of steps before the forces +reached the requested precision Fmax < 100. + +writing lowest energy coordinates. + +Steepest Descents did not converge to Fmax < 100 in 11 steps. +Potential Energy = -8.3125391e+04 +Maximum force = 2.1372287e+04 on atom 1 +Norm of force = 5.1859150e+02 + +GROMACS reminds you: "Der Ball ist rund, das Spiel dauert 90 minuten, alles andere ist Theorie" (Lola rennt) + +Starting constant volume equilibration... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NVT +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/nvt_1.mdp -c ../EM/min1.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o nvt1.tpr + +Setting the LD random seed to -1631510067 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Velocities were taken from a Maxwell distribution at 300 K +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 1 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Estimate for the relative computational load of the PME mesh part: 0.23 + +There was 1 note + +GROMACS reminds you: "No great discovery was ever made without a bold guess." (Marie Curie) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm +Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NVT +Command line: + gmx mdrun -deffnm nvt1 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file nvt1.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +50 steps, 0.1 ps. + +Writing final coordinates. + + Core t (s) Wall t (s) (%) + Time: 1.273 0.318 399.9 + (ns/day) (hour/ns) +Performance: 13.842 1.734 + +GROMACS reminds you: "You're like them scientists on TV explaining black holes. More you talk, less I get" (Jess Walter) + +Constant volume equilibration complete. +Starting constant pressure equilibration... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NPT +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/npt_1.mdp -c ../NVT/nvt1.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NVT/nvt1.cpt -o npt1.tpr + +Setting the LD random seed to -166230178 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 1 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Reading Coordinates, Velocities and Box size from old trajectory +Will read whole trajectory + Last frame -1 time 0.050 +Using frame at t = 0.05 ps +Starting time for run is 0 ps +Estimate for the relative computational load of the PME mesh part: 0.23 + +There was 1 note + +GROMACS reminds you: "Keep Your Shoes and Socks On, People" (F. Zappa) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm +Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NPT +Command line: + gmx mdrun -deffnm npt1 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file npt1.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +50 steps, 0.1 ps. + +Writing final coordinates. + + Core t (s) Wall t (s) (%) + Time: 1.310 0.328 399.9 + (ns/day) (hour/ns) +Performance: 13.448 1.785 + +GROMACS reminds you: "Don't Follow Me Home" (Throwing Muses) + +Constant pressure equilibration complete. +Starting production MD simulation... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/Production_MD +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_1.mdp -c ../NPT/npt1.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NPT/npt1.cpt -o md1.tpr + + +NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_1.mdp]: + With PME there is a minor soft core effect present at the cut-off, + proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on + energy conservation, but usually other effects dominate. With a common + sigma value of 0.34 nm the fraction of the particle-particle potential at + the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05. + +Setting the LD random seed to -651728442 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 2 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Reading Coordinates, Velocities and Box size from old trajectory +Will read whole trajectory + Last frame -1 time 0.050 +Using frame at t = 0.05 ps +Starting time for run is 0 ps +Estimate for the relative computational load of the PME mesh part: 0.47 + +There were 2 notes + +GROMACS reminds you: "Beat On the Brat With a Baseball Bat" (The Ramones) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm +Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/Production_MD +Command line: + gmx mdrun -deffnm md1 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file md1.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 10 to 50, rlist from 0.8 to 0.86 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +2000 steps, 2.0 ps. + +Writing final coordinates. + + Core t (s) Wall t (s) (%) + Time: 27.548 6.887 400.0 + (ns/day) (hour/ns) +Performance: 25.103 0.956 + +GROMACS reminds you: "Nothing is more anarchic than power." (Pier Paolo Pasolini) + +Production MD complete. +Ending. Job completed for lambda = 1 +Starting minimization for lambda = 2... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/EM +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/em_steep_2.mdp -c /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o min2.tpr + +Setting the LD random seed to 886887101 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet +Number of degrees of freedom in T-Coupling group rest is 12987.00 +Estimate for the relative computational load of the PME mesh part: 0.21 + +GROMACS reminds you: "Sisters Have Always Fascinated Me" (Speech) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/EM +Command line: + gmx mdrun -deffnm min2 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file min2.tpr, VERSION 2019.1 (single precision) + +Using 1 MPI thread +Using 4 OpenMP threads + + +Steepest Descents: + Tolerance (Fmax) = 1.00000e+02 + Number of steps = 10 + +Energy minimization reached the maximum number of steps before the forces +reached the requested precision Fmax < 100. + +writing lowest energy coordinates. + +Steepest Descents did not converge to Fmax < 100 in 11 steps. +Potential Energy = -8.3125391e+04 +Maximum force = 2.1372287e+04 on atom 1 +Norm of force = 5.1859150e+02 + +GROMACS reminds you: "The Candlelight Was Just Right" (Beastie Boys) + +Starting constant volume equilibration... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NVT +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/nvt_2.mdp -c ../EM/min2.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o nvt2.tpr + +Setting the LD random seed to -902054215 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Velocities were taken from a Maxwell distribution at 300 K +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 1 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Estimate for the relative computational load of the PME mesh part: 0.23 + +There was 1 note + +GROMACS reminds you: "I spent a lot of money on booze, birds and fast cars. The rest I just squandered." (George Best) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm +Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NVT +Command line: + gmx mdrun -deffnm nvt2 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file nvt2.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +50 steps, 0.1 ps. + +Writing final coordinates. + + Core t (s) Wall t (s) (%) + Time: 1.308 0.327 399.9 + (ns/day) (hour/ns) +Performance: 13.471 1.782 + +GROMACS reminds you: "What if you're wrong about the great Ju Ju at the bottom of the sea?" (Richard Dawkins) + +Constant volume equilibration complete. +Starting constant pressure equilibration... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NPT +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/npt_2.mdp -c ../NVT/nvt2.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NVT/nvt2.cpt -o npt2.tpr + +Setting the LD random seed to -652502066 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 1 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Reading Coordinates, Velocities and Box size from old trajectory +Will read whole trajectory + Last frame -1 time 0.050 +Using frame at t = 0.05 ps +Starting time for run is 0 ps +Estimate for the relative computational load of the PME mesh part: 0.23 + +There was 1 note + +GROMACS reminds you: "When doing HPC, don't communica" (Jim Demmel) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm +Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NPT +Command line: + gmx mdrun -deffnm npt2 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file npt2.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 20 to 100, rlist from 1.2 to 1.2 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +50 steps, 0.1 ps. + +Writing final coordinates. + + Core t (s) Wall t (s) (%) + Time: 1.290 0.323 399.9 + (ns/day) (hour/ns) +Performance: 13.659 1.757 + +GROMACS reminds you: "People are DNA's way of making more DNA." (Edward O. Wilson) + +Constant pressure equilibration complete. +Starting production MD simulation... + :-) GROMACS - gmx grompp, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx grompp, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/Production_MD +Command line: + gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_2.mdp -c ../NPT/npt2.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NPT/npt2.cpt -o md2.tpr + + +NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_2.mdp]: + With PME there is a minor soft core effect present at the cut-off, + proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on + energy conservation, but usually other effects dominate. With a common + sigma value of 0.34 nm the fraction of the particle-particle potential at + the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05. + +Setting the LD random seed to 551042888 +Generated 45 of the 45 non-bonded parameter combinations +Generating 1-4 interactions: fudge = 0.5 +Generated 45 of the 45 1-4 parameter combinations +Excluding 3 bonded neighbours molecule type 'Merged_Molecule' +Excluding 3 bonded neighbours molecule type 'NA' +Excluding 3 bonded neighbours molecule type 'CL' +Excluding 3 bonded neighbours molecule type 'WAT' +Removing all charge groups because cutoff-scheme=Verlet + +NOTE 2 [file morph.top, line 232]: + The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has + an estimated oscillational period of 8.0e-03 ps, which is less than 10 + times the time step of 1.0e-03 ps. + Maybe you forgot to change the constraints mdp option. + +Number of degrees of freedom in T-Coupling group System is 12987.00 +Reading Coordinates, Velocities and Box size from old trajectory +Will read whole trajectory + Last frame -1 time 0.050 +Using frame at t = 0.05 ps +Starting time for run is 0 ps +Estimate for the relative computational load of the PME mesh part: 0.47 + +There were 2 notes + +GROMACS reminds you: "Wedged as we are between two eternities of idleness, there is no excuse for being idle now" (Anthony Burgess) + +Analysing residue names: +There are: 1 Other residues +There are: 10 Ion residues +There are: 2151 Water residues +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... +Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K +Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm +Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm +Note that mdrun will redetermine rlist based on the actual pair-list setup +Calculating fourier grid dimensions for X Y Z +Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096 +This run will generate roughly 1 Mb of data + :-) GROMACS - gmx mdrun, 2019.1 (-: + + GROMACS is written by: + Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen + Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd + Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray + Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang + Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis + Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson + Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund + Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall + Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov + Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen + Christian Wennberg Maarten Wolf + and the project leaders: + Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel + +Copyright (c) 1991-2000, University of Groningen, The Netherlands. +Copyright (c) 2001-2018, The GROMACS development team at +Uppsala University, Stockholm University and +the Royal Institute of Technology, Sweden. +check out http://www.gromacs.org for more information. + +GROMACS is free software; you can redistribute it and/or modify it +under the terms of the GNU Lesser General Public License +as published by the Free Software Foundation; either version 2.1 +of the License, or (at your option) any later version. + +GROMACS: gmx mdrun, version 2019.1 +Executable: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx +Data prefix: /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1 +Working dir: /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/Production_MD +Command line: + gmx mdrun -deffnm md2 + +Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). +The current CPU can measure timings more accurately than the code in +gmx mdrun was configured to use. This might affect your simulation +speed as accurate timings are needed for load-balancing. +Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. +Reading file md2.tpr, VERSION 2019.1 (single precision) +Changing nstlist from 10 to 50, rlist from 0.8 to 0.86 + + +Using 1 MPI thread +Using 4 OpenMP threads + +starting mdrun 'BioSimSpace System' +2000 steps, 2.0 ps. + +step 2: One or more water molecules can not be settled. +Check for bad contacts and/or reduce the timestep if appropriate. +Wrote pdb files with previous and current coordinates + +WARNING: Listed nonbonded interaction between particles 6 and 15 +at distance 47.750 which is larger than the table limit 1.860 nm. + +This is likely either a 1,4 interaction, or a listed interaction inside +a smaller molecule you are decoupling during a free energy calculation. +Since interactions at distances beyond the table cannot be computed, +they are skipped until they are inside the table limit again. You will +only see this message once, even if it occurs for several interactions. + +IMPORTANT: This should not happen in a stable simulation, so there is +probably something wrong with your system. Only change the table-extension +distance in the mdp file if you are really sure that is the reason. + + + +WARNING: Listed nonbonded interaction between particles 2 and 15 +at distance 47.627 which is larger than the table limit 1.860 nm. + +This is likely either a 1,4 interaction, or a listed interaction inside +a smaller molecule you are decoupling during a free energy calculation. +Since interactions at distances beyond the table cannot be computed, +they are skipped until they are inside the table limit again. You will +only see this message once, even if it occurs for several interactions. + +IMPORTANT: This should not happen in a stable simulation, so there is +probably something wrong with your system. Only change the table-extension +distance in the mdp file if you are really sure that is the reason. + + +/scratch2/tsenapathi/Projects/BRIDGE/galaxy-tools-compchem/tools/free_energy/alchemical_run/gmx_fep.sh: line 104: 13890 Segmentation fault gmx mdrun -deffnm md$LAMBDA +Production MD complete. +Ending. Job completed for lambda = 2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alchemical_run/test-data/morph.gro Mon Nov 11 13:20:39 2019 -0500 @@ -0,0 +1,6484 @@ +GROningen MAchine for Chemical Simulation + 6481 + 1LIG C 1 1.955 1.939 2.023 + 1LIG C1 2 1.997 1.913 1.895 + 1LIG C2 3 2.091 1.992 1.835 + 1LIG C3 4 2.141 2.098 1.902 + 1LIG C4 5 2.099 2.126 2.030 + 1LIG C5 6 2.007 2.044 2.092 + 1LIG H 7 1.881 1.875 2.069 + 1LIG H1 8 1.955 1.829 1.841 + 1LIG H2 9 2.124 1.970 1.734 + 1LIG H3 10 2.215 2.162 1.854 + 1LIG H4 11 2.140 2.211 2.084 + 1LIG H5 12 1.975 2.064 2.193 + 1LIG H 13 1.838 1.789 2.010 + 1LIG H1 14 1.921 1.817 2.156 + 1LIG H2 15 1.786 1.927 2.095 + 1LIG H7 16 2.022 2.150 2.248 + 1LIG H8 17 1.868 2.096 2.200 + 1LIG H9 18 1.999 1.983 2.266 + 2NA NA 19 0.461 1.266 1.727 + 3NA NA 20 0.225 2.137 2.858 + 4NA NA 21 1.400 3.831 0.426 + 5NA NA 22 0.614 3.846 1.979 + 6NA NA 23 2.064 2.147 3.360 + 7CL CL 24 1.730 0.934 1.517 + 8CL CL 25 0.594 0.745 2.514 + 9CL CL 26 0.473 4.224 3.915 + 10CL CL 27 2.721 1.374 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2.084 1.147 + 552WAT H1 1650 0.599 2.000 1.184 + 552WAT H2 1651 0.473 2.103 1.191 + 553WAT O 1652 0.866 2.316 0.642 + 553WAT H1 1653 0.834 2.388 0.580 + 553WAT H2 1654 0.890 2.235 0.589 + 554WAT O 1655 1.017 1.901 0.753 + 554WAT H1 1656 0.945 1.906 0.684 + 554WAT H2 1657 0.993 1.832 0.822 + 555WAT O 1658 1.429 3.035 0.867 + 555WAT H1 1659 1.374 2.951 0.860 + 555WAT H2 1660 1.455 3.064 0.775 + 556WAT O 1661 1.466 2.452 0.992 + 556WAT H1 1662 1.436 2.357 0.999 + 556WAT H2 1663 1.539 2.468 1.058 + 557WAT O 1664 1.857 2.695 0.377 + 557WAT H1 1665 1.899 2.631 0.441 + 557WAT H2 1666 1.819 2.644 0.299 + 558WAT O 1667 0.488 3.247 0.174 + 558WAT H1 1668 0.401 3.232 0.221 + 558WAT H2 1669 0.471 3.273 0.079 + 559WAT O 1670 1.664 3.142 0.657 + 559WAT H1 1671 1.763 3.150 0.671 + 559WAT H2 1672 1.619 3.226 0.688 + 560WAT O 1673 1.390 2.437 0.078 + 560WAT H1 1674 1.336 2.416 0.159 + 560WAT H2 1675 1.481 2.396 0.087 + 561WAT O 1676 0.527 2.118 0.328 + 561WAT H1 1677 0.554 2.059 0.253 + 561WAT H2 1678 0.527 2.213 0.297 + 562WAT O 1679 1.754 3.085 1.588 + 562WAT H1 1680 1.845 3.046 1.575 + 562WAT H2 1681 1.762 3.181 1.612 + 563WAT O 1682 1.064 3.209 1.340 + 563WAT H1 1683 0.984 3.186 1.395 + 563WAT H2 1684 1.147 3.183 1.389 + 564WAT O 1685 1.592 3.491 1.625 + 564WAT H1 1686 1.619 3.525 1.535 + 564WAT H2 1687 1.671 3.453 1.671 + 565WAT O 1688 1.111 3.057 1.100 + 565WAT H1 1689 1.071 3.101 1.181 + 565WAT H2 1690 1.070 3.094 1.017 + 566WAT O 1691 1.638 2.961 1.079 + 566WAT H1 1692 1.643 3.042 1.138 + 566WAT H2 1693 1.552 2.963 1.028 + 567WAT O 1694 0.915 1.951 1.402 + 567WAT H1 1695 0.940 1.931 1.307 + 567WAT H2 1696 0.987 2.007 1.444 + 568WAT O 1697 0.980 2.978 1.719 + 568WAT H1 1698 0.881 2.984 1.729 + 568WAT H2 1699 1.003 2.898 1.663 + 569WAT O 1700 0.705 2.912 0.368 + 569WAT H1 1701 0.691 2.919 0.467 + 569WAT H2 1702 0.789 2.861 0.350 + 570WAT O 1703 0.410 2.675 1.251 + 570WAT H1 1704 0.496 2.687 1.301 + 570WAT H2 1705 0.368 2.588 1.278 + 571WAT O 1706 1.274 2.248 1.262 + 571WAT H1 1707 1.295 2.322 1.326 + 571WAT H2 1708 1.185 2.265 1.219 + 572WAT O 1709 0.064 3.426 1.331 + 572WAT H1 1710 0.018 3.508 1.297 + 572WAT H2 1711 0.162 3.445 1.340 + 573WAT O 1712 0.367 2.962 0.501 + 573WAT H1 1713 0.360 3.045 0.445 + 573WAT H2 1714 0.371 2.882 0.441 + 574WAT O 1715 0.566 2.399 0.865 + 574WAT H1 1716 0.578 2.465 0.791 + 574WAT H2 1717 0.612 2.433 0.948 + 575WAT O 1718 1.252 3.210 0.388 + 575WAT H1 1719 1.302 3.287 0.428 + 575WAT H2 1720 1.157 3.212 0.420 + 576WAT O 1721 1.272 3.307 1.142 + 576WAT H1 1722 1.319 3.320 1.229 + 576WAT H2 1723 1.206 3.233 1.151 + 577WAT O 1724 1.582 2.501 0.472 + 577WAT H1 1725 1.551 2.562 0.545 + 577WAT H2 1726 1.632 2.553 0.403 + 578WAT O 1727 0.354 3.372 1.329 + 578WAT H1 1728 0.333 3.328 1.242 + 578WAT H2 1729 0.451 3.398 1.332 + 579WAT O 1730 0.402 2.613 1.598 + 579WAT H1 1731 0.470 2.668 1.551 + 579WAT H2 1732 0.442 2.525 1.625 + 580WAT O 1733 1.587 2.641 1.670 + 580WAT H1 1734 1.495 2.679 1.665 + 580WAT H2 1735 1.647 2.688 1.605 + 581WAT O 1736 1.013 1.967 1.770 + 581WAT H1 1737 1.019 2.052 1.718 + 581WAT H2 1738 1.045 1.891 1.713 + 582WAT O 1739 0.504 1.912 1.740 + 582WAT H1 1740 0.462 1.855 1.670 + 582WAT H2 1741 0.438 1.981 1.772 + 583WAT O 1742 0.573 2.732 1.029 + 583WAT H1 1743 0.617 2.821 1.020 + 583WAT H2 1744 0.510 2.732 1.106 + 584WAT O 1745 1.360 2.724 1.045 + 584WAT H1 1746 1.285 2.724 0.979 + 584WAT H2 1747 1.397 2.632 1.054 + 585WAT O 1748 1.209 2.387 0.275 + 585WAT H1 1749 1.222 2.303 0.329 + 585WAT H2 1750 1.180 2.461 0.335 + 586WAT O 1751 0.307 2.075 1.231 + 586WAT H1 1752 0.284 2.112 1.321 + 586WAT H2 1753 0.277 1.980 1.225 + 587WAT O 1754 0.037 3.172 1.282 + 587WAT H1 1755 0.090 3.123 1.350 + 587WAT H2 1756 0.059 3.270 1.287 + 588WAT O 1757 0.732 2.496 1.064 + 588WAT H1 1758 0.791 2.470 0.988 + 588WAT H2 1759 0.704 2.592 1.053 + 589WAT O 1760 1.728 2.797 1.854 + 589WAT H1 1761 1.682 2.790 1.765 + 589WAT H2 1762 1.666 2.841 1.920 + 590WAT O 1763 0.307 1.925 0.618 + 590WAT H1 1764 0.296 2.019 0.651 + 590WAT H2 1765 0.302 1.862 0.695 + 591WAT O 1766 1.622 2.229 0.374 + 591WAT H1 1767 1.624 2.153 0.438 + 591WAT H2 1768 1.574 2.306 0.414 + 592WAT O 1769 1.023 2.628 0.966 + 592WAT H1 1770 1.038 2.649 1.062 + 592WAT H2 1771 0.993 2.533 0.957 + 593WAT O 1772 0.980 3.435 1.700 + 593WAT H1 1773 0.960 3.479 1.612 + 593WAT H2 1774 1.019 3.344 1.684 + 594WAT O 1775 1.859 3.380 1.605 + 594WAT H1 1776 1.873 3.407 1.510 + 594WAT H2 1777 1.942 3.402 1.658 + 595WAT O 1778 0.350 2.760 1.804 + 595WAT H1 1779 0.426 2.804 1.852 + 595WAT H2 1780 0.385 2.713 1.722 + 596WAT O 1781 1.540 2.136 0.125 + 596WAT H1 1782 1.479 2.061 0.148 + 596WAT H2 1783 1.562 2.188 0.208 + 597WAT O 1784 1.303 2.700 0.042 + 597WAT H1 1785 1.337 2.607 0.057 + 597WAT H2 1786 1.321 2.727 -0.053 + 598WAT O 1787 1.068 3.195 0.849 + 598WAT H1 1788 1.075 3.111 0.794 + 598WAT H2 1789 1.130 3.264 0.813 + 599WAT O 1790 0.319 2.672 0.949 + 599WAT H1 1791 0.412 2.708 0.954 + 599WAT H2 1792 0.313 2.587 1.001 + 600WAT O 1793 0.339 2.371 1.006 + 600WAT H1 1794 0.287 2.288 0.989 + 600WAT H2 1795 0.416 2.376 0.942 + 601WAT O 1796 1.138 2.242 1.678 + 601WAT H1 1797 1.093 2.305 1.742 + 601WAT H2 1798 1.231 2.273 1.661 + 602WAT O 1799 1.160 2.069 1.477 + 602WAT H1 1800 1.160 2.133 1.554 + 602WAT H2 1801 1.188 2.117 1.394 + 603WAT O 1802 0.008 3.188 0.200 + 603WAT H1 1803 -0.085 3.209 0.169 + 603WAT H2 1804 0.018 3.089 0.213 + 604WAT O 1805 0.088 3.663 0.927 + 604WAT H1 1806 0.046 3.577 0.900 + 604WAT H2 1807 0.182 3.666 0.893 + 605WAT O 1808 0.504 3.430 0.910 + 605WAT H1 1809 0.570 3.504 0.919 + 605WAT H2 1810 0.548 3.351 0.868 + 606WAT O 1811 1.002 2.658 1.238 + 606WAT H1 1812 1.043 2.626 1.324 + 606WAT H2 1813 0.906 2.631 1.235 + 607WAT O 1814 0.040 2.406 1.114 + 607WAT H1 1815 0.125 2.373 1.073 + 607WAT H2 1816 0.053 2.421 1.212 + 608WAT O 1817 0.189 2.382 1.722 + 608WAT H1 1818 0.248 2.342 1.652 + 608WAT H2 1819 0.131 2.453 1.681 + 609WAT O 1820 1.369 2.812 1.660 + 609WAT H1 1821 1.408 2.901 1.680 + 609WAT H2 1822 1.379 2.792 1.563 + 610WAT O 1823 0.815 2.434 0.325 + 610WAT H1 1824 0.822 2.345 0.279 + 610WAT H2 1825 0.721 2.468 0.317 + 611WAT O 1826 1.657 2.466 1.206 + 611WAT H1 1827 1.619 2.397 1.268 + 611WAT H2 1828 1.739 2.430 1.162 + 612WAT O 1829 0.252 3.426 1.744 + 612WAT H1 1830 0.222 3.483 1.820 + 612WAT H2 1831 0.245 3.329 1.770 + 613WAT O 1832 0.671 2.326 1.269 + 613WAT H1 1833 0.637 2.237 1.239 + 613WAT H2 1834 0.697 2.380 1.189 + 614WAT O 1835 0.930 3.540 1.465 + 614WAT H1 1836 0.906 3.522 1.370 + 614WAT H2 1837 0.960 3.634 1.475 + 615WAT O 1838 0.473 2.362 0.191 + 615WAT H1 1839 0.534 2.442 0.195 + 615WAT H2 1840 0.378 2.393 0.198 + 616WAT O 1841 0.159 2.999 1.466 + 616WAT H1 1842 0.181 2.938 1.542 + 616WAT H2 1843 0.169 2.950 1.380 + 617WAT O 1844 1.347 2.921 1.234 + 617WAT H1 1845 1.371 2.858 1.160 + 617WAT H2 1846 1.257 2.961 1.216 + 618WAT O 1847 1.302 2.717 0.309 + 618WAT H1 1848 1.216 2.686 0.351 + 618WAT H2 1849 1.298 2.703 0.210 + 619WAT O 1850 1.759 3.609 1.154 + 619WAT H1 1851 1.820 3.639 1.081 + 619WAT H2 1852 1.721 3.520 1.132 + 620WAT O 1853 1.252 3.593 1.128 + 620WAT H1 1854 1.336 3.598 1.074 + 620WAT H2 1855 1.229 3.497 1.146 + 621WAT O 1856 0.083 3.120 1.022 + 621WAT H1 1857 0.078 3.119 1.122 + 621WAT H2 1858 0.000 3.079 0.984 + 622WAT O 1859 0.688 3.524 1.716 + 622WAT H1 1860 0.632 3.605 1.725 + 622WAT H2 1861 0.740 3.528 1.630 + 623WAT O 1862 0.903 1.948 0.133 + 623WAT H1 1863 0.954 1.949 0.047 + 623WAT H2 1864 0.959 1.906 0.204 + 624WAT O 1865 1.726 1.997 0.523 + 624WAT H1 1866 1.799 1.980 0.456 + 624WAT H2 1867 1.695 1.910 0.561 + 625WAT O 1868 1.388 3.435 0.477 + 625WAT H1 1869 1.455 3.447 0.403 + 625WAT H2 1870 1.348 3.524 0.500 + 626WAT O 1871 0.130 3.656 1.851 + 626WAT H1 1872 0.089 3.582 1.904 + 626WAT H2 1873 0.194 3.707 1.909 + 627WAT O 1874 1.280 2.789 0.672 + 627WAT H1 1875 1.340 2.708 0.674 + 627WAT H2 1876 1.320 2.858 0.612 + 628WAT O 1877 0.830 3.135 1.422 + 628WAT H1 1878 0.825 3.168 1.517 + 628WAT H2 1879 0.744 3.154 1.376 + 629WAT O 1880 0.672 3.478 0.154 + 629WAT H1 1881 0.681 3.488 0.055 + 629WAT H2 1882 0.632 3.389 0.175 + 630WAT O 1883 1.650 3.582 1.394 + 630WAT H1 1884 1.703 3.592 1.310 + 630WAT H2 1885 1.623 3.672 1.428 + 631WAT O 1886 1.841 2.037 0.963 + 631WAT H1 1887 1.880 1.952 0.927 + 631WAT H2 1888 1.743 2.039 0.944 + 632WAT O 1889 0.263 2.188 0.720 + 632WAT H1 1890 0.184 2.239 0.686 + 632WAT H2 1891 0.254 2.173 0.818 + 633WAT O 1892 1.194 3.474 0.031 + 633WAT H1 1893 1.200 3.381 0.068 + 633WAT H2 1894 1.135 3.474 -0.049 + 634WAT O 1895 0.822 2.864 1.372 + 634WAT H1 1896 0.862 2.863 1.280 + 634WAT H2 1897 0.832 2.956 1.412 + 635WAT O 1898 0.916 2.772 0.291 + 635WAT H1 1899 0.979 2.810 0.223 + 635WAT H2 1900 0.956 2.689 0.330 + 636WAT O 1901 1.504 3.469 0.044 + 636WAT H1 1902 1.412 3.506 0.051 + 636WAT H2 1903 1.542 3.489 -0.046 + 637WAT O 1904 0.372 3.150 1.490 + 637WAT H1 1905 0.359 3.243 1.456 + 637WAT H2 1906 0.288 3.098 1.477 + 638WAT O 1907 1.614 3.154 1.289 + 638WAT H1 1908 1.674 3.157 1.369 + 638WAT H2 1909 1.539 3.218 1.302 + 639WAT O 1910 1.039 2.960 0.696 + 639WAT H1 1911 0.969 2.913 0.750 + 639WAT H2 1912 1.098 2.892 0.653 + 640WAT O 1913 1.014 2.098 0.971 + 640WAT H1 1914 1.006 2.062 0.878 + 640WAT H2 1915 1.012 2.022 1.036 + 641WAT O 1916 0.590 3.349 0.491 + 641WAT H1 1917 0.632 3.291 0.421 + 641WAT H2 1918 0.546 3.428 0.447 + 642WAT O 1919 1.709 2.247 1.381 + 642WAT H1 1920 1.782 2.316 1.385 + 642WAT H2 1921 1.737 2.172 1.322 + 643WAT O 1922 0.255 3.210 0.290 + 643WAT H1 1923 0.159 3.211 0.263 + 643WAT H2 1924 0.267 3.263 0.374 + 644WAT O 1925 0.105 2.875 1.726 + 644WAT H1 1926 0.028 2.842 1.780 + 644WAT H2 1927 0.190 2.845 1.768 + 645WAT O 1928 0.672 2.065 1.489 + 645WAT H1 1929 0.762 2.049 1.449 + 645WAT H2 1930 0.680 2.070 1.588 + 646WAT O 1931 0.075 2.207 0.033 + 646WAT H1 1932 -0.017 2.179 0.004 + 646WAT H2 1933 0.106 2.284 -0.023 + 647WAT O 1934 1.440 2.718 1.398 + 647WAT H1 1935 1.383 2.770 1.335 + 647WAT H2 1936 1.536 2.730 1.374 + 648WAT O 1937 0.072 2.028 0.318 + 648WAT H1 1938 0.055 2.111 0.264 + 648WAT H2 1939 0.162 1.991 0.296 + 649WAT O 1940 1.183 3.197 0.119 + 649WAT H1 1941 1.084 3.186 0.121 + 649WAT H2 1942 1.217 3.212 0.212 + 650WAT O 1943 0.613 2.704 1.431 + 650WAT H1 1944 0.669 2.785 1.414 + 650WAT H2 1945 0.672 2.624 1.434 + 651WAT O 1946 1.493 3.629 0.959 + 651WAT H1 1947 1.526 3.693 0.890 + 651WAT H2 1948 1.559 3.623 1.034 + 652WAT O 1949 0.716 2.427 1.708 + 652WAT H1 1950 0.735 2.492 1.782 + 652WAT H2 1951 0.776 2.347 1.717 + 653WAT O 1952 1.450 3.082 1.633 + 653WAT H1 1953 1.441 3.072 1.732 + 653WAT H2 1954 1.546 3.075 1.607 + 654WAT O 1955 0.390 3.603 1.560 + 654WAT H1 1956 0.299 3.644 1.558 + 654WAT H2 1957 0.383 3.509 1.592 + 655WAT O 1958 1.674 2.745 1.254 + 655WAT H1 1959 1.647 2.656 1.217 + 655WAT H2 1960 1.675 2.813 1.181 + 656WAT O 1961 1.225 2.187 0.449 + 656WAT H1 1962 1.290 2.113 0.438 + 656WAT H2 1963 1.245 2.237 0.533 + 657WAT O 1964 0.594 2.607 0.652 + 657WAT H1 1965 0.644 2.692 0.633 + 657WAT H2 1966 0.506 2.609 0.604 + 658WAT O 1967 1.777 2.204 1.642 + 658WAT H1 1968 1.760 2.235 1.548 + 658WAT H2 1969 1.693 2.167 1.680 + 659WAT O 1970 1.730 2.796 1.517 + 659WAT H1 1971 1.768 2.887 1.532 + 659WAT H2 1972 1.722 2.779 1.418 + 660WAT O 1973 0.859 3.236 0.016 + 660WAT H1 1974 0.813 3.251 0.104 + 660WAT H2 1975 0.903 3.321 -0.014 + 661WAT O 1976 0.661 3.652 0.953 + 661WAT H1 1977 0.615 3.740 0.940 + 661WAT H2 1978 0.760 3.664 0.946 + 662WAT O 1979 0.859 2.818 0.861 + 662WAT H1 1980 0.913 2.749 0.909 + 662WAT H2 1981 0.827 2.887 0.927 + 663WAT O 1982 1.083 2.846 0.087 + 663WAT H1 1983 1.060 2.899 0.005 + 663WAT H2 1984 1.164 2.790 0.068 + 664WAT O 1985 1.861 3.431 0.851 + 664WAT H1 1986 1.790 3.419 0.781 + 664WAT H2 1987 1.862 3.352 0.911 + 665WAT O 1988 0.221 3.176 1.844 + 665WAT H1 1989 0.156 3.103 1.823 + 665WAT H2 1990 0.225 3.190 1.942 + 666WAT O 1991 0.079 3.102 0.653 + 666WAT H1 1992 0.078 3.055 0.741 + 666WAT H2 1993 0.161 3.074 0.602 + 667WAT O 1994 0.672 3.253 1.624 + 667WAT H1 1995 0.594 3.203 1.662 + 667WAT H2 1996 0.669 3.348 1.655 + 668WAT O 1997 1.824 2.054 1.227 + 668WAT H1 1998 1.820 1.964 1.271 + 668WAT H2 1999 1.827 2.043 1.128 + 669WAT O 2000 0.428 2.286 0.520 + 669WAT H1 2001 0.458 2.214 0.458 + 669WAT H2 2002 0.389 2.246 0.603 + 670WAT O 2003 1.705 3.349 1.104 + 670WAT H1 2004 1.612 3.324 1.077 + 670WAT H2 2005 1.731 3.299 1.186 + 671WAT O 2006 0.317 2.409 1.280 + 671WAT H1 2007 0.355 2.350 1.352 + 671WAT H2 2008 0.357 2.383 1.192 + 672WAT O 2009 0.812 3.448 0.687 + 672WAT H1 2010 0.844 3.458 0.593 + 672WAT H2 2011 0.733 3.386 0.689 + 673WAT O 2012 1.424 2.076 1.112 + 673WAT H1 2013 1.476 2.011 1.167 + 673WAT H2 2014 1.375 2.139 1.173 + 674WAT O 2015 1.001 1.896 1.154 + 674WAT H1 2016 0.938 1.824 1.123 + 674WAT H2 2017 1.094 1.860 1.154 + 675WAT O 2018 0.770 3.192 0.301 + 675WAT H1 2019 0.724 3.105 0.318 + 675WAT H2 2020 0.861 3.189 0.342 + 676WAT O 2021 0.618 3.429 1.284 + 676WAT H1 2022 0.613 3.511 1.341 + 676WAT H2 2023 0.707 3.426 1.239 + 677WAT O 2024 1.352 1.914 0.168 + 677WAT H1 2025 1.387 1.873 0.084 + 677WAT H2 2026 1.262 1.876 0.188 + 678WAT O 2027 1.300 2.315 0.691 + 678WAT H1 2028 1.241 2.395 0.695 + 678WAT H2 2029 1.315 2.280 0.784 + 679WAT O 2030 1.593 2.083 0.882 + 679WAT H1 2031 1.509 2.082 0.936 + 679WAT H2 2032 1.595 2.166 0.826 + 680WAT O 2033 0.039 2.939 0.300 + 680WAT H1 2034 0.138 2.928 0.291 + 680WAT H2 2035 -0.001 2.853 0.332 + 681WAT O 2036 0.875 3.508 0.337 + 681WAT H1 2037 0.798 3.473 0.283 + 681WAT H2 2038 0.843 3.579 0.399 + 682WAT O 2039 0.230 2.490 1.975 + 682WAT H1 2040 0.137 2.488 2.012 + 682WAT H2 2041 0.231 2.451 1.883 + 683WAT O 2042 0.019 2.230 2.509 + 683WAT H1 2043 -0.063 2.273 2.548 + 683WAT H2 2044 -0.009 2.157 2.446 + 684WAT O 2045 0.569 3.137 3.027 + 684WAT H1 2046 0.476 3.130 2.990 + 684WAT H2 2047 0.580 3.226 3.071 + 685WAT O 2048 1.555 3.373 2.565 + 685WAT H1 2049 1.498 3.357 2.646 + 685WAT H2 2050 1.496 3.383 2.485 + 686WAT O 2051 1.135 2.565 2.579 + 686WAT H1 2052 1.192 2.643 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3.575 2.345 + 696WAT H1 2082 0.265 3.652 2.399 + 696WAT H2 2083 0.275 3.575 2.255 + 697WAT O 2084 1.127 3.203 3.552 + 697WAT H1 2085 1.174 3.203 3.640 + 697WAT H2 2086 1.079 3.116 3.541 + 698WAT O 2087 0.230 3.296 2.400 + 698WAT H1 2088 0.204 3.392 2.400 + 698WAT H2 2089 0.159 3.242 2.445 + 699WAT O 2090 0.240 2.953 2.748 + 699WAT H1 2091 0.254 2.869 2.800 + 699WAT H2 2092 0.185 3.017 2.803 + 700WAT O 2093 0.620 3.648 3.301 + 700WAT H1 2094 0.528 3.631 3.336 + 700WAT H2 2095 0.648 3.740 3.327 + 701WAT O 2096 0.606 2.826 1.985 + 701WAT H1 2097 0.613 2.910 1.931 + 701WAT H2 2098 0.652 2.839 2.073 + 702WAT O 2099 1.594 1.976 3.342 + 702WAT H1 2100 1.576 2.043 3.270 + 702WAT H2 2101 1.591 2.022 3.431 + 703WAT O 2102 0.122 2.505 2.425 + 703WAT H1 2103 0.077 2.417 2.442 + 703WAT H2 2104 0.121 2.559 2.509 + 704WAT O 2105 1.842 3.629 2.221 + 704WAT H1 2106 1.896 3.600 2.301 + 704WAT H2 2107 1.872 3.719 2.192 + 705WAT O 2108 0.027 3.458 1.979 + 705WAT H1 2109 0.008 3.362 2.000 + 705WAT H2 2110 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1.906 + 1843WAT H1 5523 3.274 3.506 1.913 + 1843WAT H2 5524 3.404 3.489 1.816 + 1844WAT O 5525 2.234 3.150 3.352 + 1844WAT H1 5526 2.221 3.243 3.318 + 1844WAT H2 5527 2.150 3.098 3.339 + 1845WAT O 5528 3.476 3.154 3.151 + 1845WAT H1 5529 3.536 3.157 3.231 + 1845WAT H2 5530 3.401 3.218 3.164 + 1846WAT O 5531 2.901 2.960 2.558 + 1846WAT H1 5532 2.831 2.913 2.612 + 1846WAT H2 5533 2.960 2.892 2.515 + 1847WAT O 5534 2.876 2.098 2.833 + 1847WAT H1 5535 2.868 2.062 2.740 + 1847WAT H2 5536 2.874 2.022 2.898 + 1848WAT O 5537 2.452 3.349 2.353 + 1848WAT H1 5538 2.494 3.291 2.283 + 1848WAT H2 5539 2.408 3.428 2.309 + 1849WAT O 5540 3.571 2.247 3.243 + 1849WAT H1 5541 3.644 2.316 3.247 + 1849WAT H2 5542 3.599 2.172 3.184 + 1850WAT O 5543 2.117 3.210 2.152 + 1850WAT H1 5544 2.021 3.211 2.125 + 1850WAT H2 5545 2.129 3.263 2.236 + 1851WAT O 5546 1.967 2.875 3.588 + 1851WAT H1 5547 1.890 2.842 3.642 + 1851WAT H2 5548 2.052 2.845 3.630 + 1852WAT O 5549 2.534 2.065 3.351 + 1852WAT H1 5550 2.624 2.049 3.311 + 1852WAT H2 5551 2.542 2.070 3.450 + 1853WAT O 5552 1.937 2.207 1.895 + 1853WAT H1 5553 1.845 2.179 1.866 + 1853WAT H2 5554 1.968 2.284 1.839 + 1854WAT O 5555 3.302 2.718 3.260 + 1854WAT H1 5556 3.245 2.770 3.197 + 1854WAT H2 5557 3.398 2.730 3.236 + 1855WAT O 5558 3.045 3.197 1.981 + 1855WAT H1 5559 2.946 3.186 1.983 + 1855WAT H2 5560 3.079 3.212 2.074 + 1856WAT O 5561 2.475 2.704 3.293 + 1856WAT H1 5562 2.531 2.785 3.276 + 1856WAT H2 5563 2.534 2.624 3.296 + 1857WAT O 5564 3.355 3.629 2.821 + 1857WAT H1 5565 3.388 3.693 2.752 + 1857WAT H2 5566 3.421 3.623 2.896 + 1858WAT O 5567 2.578 2.427 3.570 + 1858WAT H1 5568 2.597 2.492 3.644 + 1858WAT H2 5569 2.638 2.347 3.579 + 1859WAT O 5570 3.312 3.082 3.495 + 1859WAT H1 5571 3.303 3.072 3.594 + 1859WAT H2 5572 3.408 3.075 3.469 + 1860WAT O 5573 2.252 3.603 3.422 + 1860WAT H1 5574 2.161 3.644 3.420 + 1860WAT H2 5575 2.245 3.509 3.454 + 1861WAT O 5576 3.536 2.745 3.116 + 1861WAT H1 5577 3.509 2.656 3.079 + 1861WAT H2 5578 3.537 2.813 3.043 + 1862WAT O 5579 3.087 2.187 2.311 + 1862WAT H1 5580 3.152 2.113 2.300 + 1862WAT H2 5581 3.107 2.237 2.395 + 1863WAT O 5582 2.456 2.607 2.514 + 1863WAT H1 5583 2.506 2.692 2.495 + 1863WAT H2 5584 2.368 2.609 2.466 + 1864WAT O 5585 3.639 2.204 3.504 + 1864WAT H1 5586 3.622 2.235 3.410 + 1864WAT H2 5587 3.555 2.167 3.542 + 1865WAT O 5588 3.592 2.796 3.379 + 1865WAT H1 5589 3.630 2.887 3.394 + 1865WAT H2 5590 3.584 2.779 3.280 + 1866WAT O 5591 2.721 3.236 1.878 + 1866WAT H1 5592 2.675 3.251 1.966 + 1866WAT H2 5593 2.765 3.321 1.848 + 1867WAT O 5594 2.523 3.652 2.815 + 1867WAT H1 5595 2.477 3.740 2.802 + 1867WAT H2 5596 2.622 3.664 2.808 + 1868WAT O 5597 2.721 2.818 2.723 + 1868WAT H1 5598 2.775 2.749 2.771 + 1868WAT H2 5599 2.689 2.887 2.789 + 1869WAT O 5600 2.945 2.846 1.949 + 1869WAT H1 5601 2.922 2.899 1.867 + 1869WAT H2 5602 3.026 2.790 1.930 + 1870WAT O 5603 3.723 3.431 2.713 + 1870WAT H1 5604 3.652 3.419 2.643 + 1870WAT H2 5605 3.724 3.352 2.773 + 1871WAT O 5606 2.083 3.176 3.706 + 1871WAT H1 5607 2.018 3.103 3.685 + 1871WAT H2 5608 2.087 3.190 3.804 + 1872WAT O 5609 1.941 3.102 2.515 + 1872WAT H1 5610 1.940 3.055 2.603 + 1872WAT H2 5611 2.023 3.074 2.464 + 1873WAT O 5612 2.534 3.253 3.486 + 1873WAT H1 5613 2.456 3.203 3.524 + 1873WAT H2 5614 2.531 3.348 3.517 + 1874WAT O 5615 3.686 2.054 3.089 + 1874WAT H1 5616 3.682 1.964 3.133 + 1874WAT H2 5617 3.689 2.043 2.990 + 1875WAT O 5618 2.290 2.286 2.382 + 1875WAT H1 5619 2.320 2.214 2.320 + 1875WAT H2 5620 2.251 2.246 2.465 + 1876WAT O 5621 3.567 3.349 2.966 + 1876WAT H1 5622 3.474 3.324 2.939 + 1876WAT H2 5623 3.593 3.299 3.048 + 1877WAT O 5624 2.179 2.409 3.142 + 1877WAT H1 5625 2.217 2.350 3.214 + 1877WAT H2 5626 2.219 2.383 3.054 + 1878WAT O 5627 2.674 3.448 2.549 + 1878WAT H1 5628 2.706 3.458 2.455 + 1878WAT H2 5629 2.595 3.386 2.551 + 1879WAT O 5630 3.286 2.076 2.974 + 1879WAT H1 5631 3.338 2.011 3.029 + 1879WAT H2 5632 3.237 2.139 3.035 + 1880WAT O 5633 2.863 1.896 3.016 + 1880WAT H1 5634 2.800 1.824 2.985 + 1880WAT H2 5635 2.956 1.860 3.016 + 1881WAT O 5636 2.632 3.192 2.163 + 1881WAT H1 5637 2.586 3.105 2.180 + 1881WAT H2 5638 2.723 3.189 2.204 + 1882WAT O 5639 2.480 3.429 3.146 + 1882WAT H1 5640 2.475 3.511 3.203 + 1882WAT H2 5641 2.569 3.426 3.101 + 1883WAT O 5642 3.214 1.914 2.030 + 1883WAT H1 5643 3.249 1.873 1.946 + 1883WAT H2 5644 3.124 1.876 2.050 + 1884WAT O 5645 3.162 2.315 2.553 + 1884WAT H1 5646 3.103 2.395 2.557 + 1884WAT H2 5647 3.177 2.280 2.646 + 1885WAT O 5648 3.455 2.083 2.744 + 1885WAT H1 5649 3.371 2.082 2.798 + 1885WAT H2 5650 3.457 2.166 2.688 + 1886WAT O 5651 1.901 2.939 2.162 + 1886WAT H1 5652 2.000 2.928 2.153 + 1886WAT H2 5653 1.861 2.853 2.194 + 1887WAT O 5654 2.737 3.508 2.199 + 1887WAT H1 5655 2.660 3.473 2.145 + 1887WAT H2 5656 2.705 3.579 2.261 + 1888WAT O 5657 2.092 2.490 3.837 + 1888WAT H1 5658 1.999 2.488 3.874 + 1888WAT H2 5659 2.093 2.451 3.745 + 1889WAT O 5660 3.617 2.469 3.955 + 1889WAT H1 5661 3.605 2.456 3.856 + 1889WAT H2 5662 3.587 2.388 4.004 + 1890WAT O 5663 2.093 3.575 4.207 + 1890WAT H1 5664 2.127 3.652 4.261 + 1890WAT H2 5665 2.137 3.575 4.117 + 1891WAT O 5666 2.468 2.826 3.847 + 1891WAT H1 5667 2.475 2.910 3.793 + 1891WAT H2 5668 2.514 2.839 3.935 + 1892WAT O 5669 1.889 3.458 3.841 + 1892WAT H1 5670 1.870 3.362 3.862 + 1892WAT H2 5671 1.856 3.516 3.916 + 1893WAT O 5672 3.387 2.861 3.914 + 1893WAT H1 5673 3.324 2.785 3.927 + 1893WAT H2 5674 3.435 2.879 4.000 + 1894WAT O 5675 2.460 2.591 3.994 + 1894WAT H1 5676 2.484 2.660 3.926 + 1894WAT H2 5677 2.382 2.624 4.048 + 1895WAT O 5678 2.727 2.210 3.919 + 1895WAT H1 5679 2.786 2.273 3.870 + 1895WAT H2 5680 2.746 2.116 3.890 + 1896WAT O 5681 2.870 3.318 4.201 + 1896WAT H1 5682 2.824 3.390 4.149 + 1896WAT H2 5683 2.866 3.338 4.299 + 1897WAT O 5684 2.183 2.805 3.966 + 1897WAT H1 5685 2.265 2.844 3.924 + 1897WAT H2 5686 2.156 2.723 3.917 + 1898WAT O 5687 2.973 3.638 3.961 + 1898WAT H1 5688 2.913 3.576 4.011 + 1898WAT H2 5689 3.004 3.594 3.876 + 1899WAT O 5690 3.494 3.239 3.805 + 1899WAT H1 5691 3.462 3.333 3.795 + 1899WAT H2 5692 3.418 3.176 3.793 + 1900WAT O 5693 2.326 3.605 4.047 + 1900WAT H1 5694 2.359 3.644 4.133 + 1900WAT H2 5695 2.402 3.598 3.982 + 1901WAT O 5696 2.476 1.984 3.841 + 1901WAT H1 5697 2.574 1.962 3.848 + 1901WAT H2 5698 2.445 1.967 3.748 + 1902WAT O 5699 3.296 3.050 3.765 + 1902WAT H1 5700 3.328 2.974 3.822 + 1902WAT H2 5701 3.204 3.077 3.795 + 1903WAT O 5702 2.159 1.897 3.895 + 1903WAT H1 5703 2.208 1.981 3.874 + 1903WAT H2 5704 2.221 1.832 3.940 + 1904WAT O 5705 2.894 2.411 3.740 + 1904WAT H1 5706 2.853 2.493 3.701 + 1904WAT H2 5707 2.958 2.437 3.813 + 1905WAT O 5708 3.719 2.695 4.101 + 1905WAT H1 5709 3.761 2.631 4.165 + 1905WAT H2 5710 3.681 2.644 4.023 + 1906WAT O 5711 2.350 3.247 3.898 + 1906WAT H1 5712 2.263 3.232 3.945 + 1906WAT H2 5713 2.333 3.273 3.803 + 1907WAT O 5714 3.252 2.437 3.802 + 1907WAT H1 5715 3.198 2.416 3.883 + 1907WAT H2 5716 3.343 2.396 3.811 + 1908WAT O 5717 3.444 2.501 4.196 + 1908WAT H1 5718 3.413 2.562 4.269 + 1908WAT H2 5719 3.494 2.553 4.127 + 1909WAT O 5720 3.402 2.136 3.849 + 1909WAT H1 5721 3.341 2.061 3.872 + 1909WAT H2 5722 3.424 2.188 3.932 + 1910WAT O 5723 3.165 2.700 3.766 + 1910WAT H1 5724 3.199 2.607 3.781 + 1910WAT H2 5725 3.183 2.727 3.671 + 1911WAT O 5726 1.870 3.188 3.924 + 1911WAT H1 5727 1.777 3.209 3.893 + 1911WAT H2 5728 1.880 3.089 3.937 + 1912WAT O 5729 2.677 2.434 4.049 + 1912WAT H1 5730 2.684 2.345 4.003 + 1912WAT H2 5731 2.583 2.468 4.041 + 1913WAT O 5732 2.335 2.362 3.915 + 1913WAT H1 5733 2.396 2.442 3.919 + 1913WAT H2 5734 2.240 2.393 3.922 + 1914WAT O 5735 3.588 1.997 4.247 + 1914WAT H1 5736 3.661 1.980 4.180 + 1914WAT H2 5737 3.557 1.910 4.285 + 1915WAT O 5738 2.534 3.478 3.878 + 1915WAT H1 5739 2.543 3.488 3.779 + 1915WAT H2 5740 2.494 3.389 3.899 + 1916WAT O 5741 3.056 3.474 3.755 + 1916WAT H1 5742 3.062 3.381 3.792 + 1916WAT H2 5743 2.997 3.474 3.675 + 1917WAT O 5744 3.366 3.469 3.768 + 1917WAT H1 5745 3.274 3.506 3.775 + 1917WAT H2 5746 3.404 3.489 3.678 + 1918WAT O 5747 2.117 3.210 4.014 + 1918WAT H1 5748 2.021 3.211 3.987 + 1918WAT H2 5749 2.129 3.263 4.098 + 1919WAT O 5750 1.937 2.207 3.757 + 1919WAT H1 5751 1.845 2.179 3.728 + 1919WAT H2 5752 1.968 2.284 3.701 + 1920WAT O 5753 3.045 3.197 3.843 + 1920WAT H1 5754 2.946 3.186 3.845 + 1920WAT H2 5755 3.079 3.212 3.936 + 1921WAT O 5756 2.721 3.236 3.740 + 1921WAT H1 5757 2.675 3.251 3.828 + 1921WAT H2 5758 2.765 3.321 3.710 + 1922WAT O 5759 2.945 2.846 3.811 + 1922WAT H1 5760 2.922 2.899 3.729 + 1922WAT H2 5761 3.026 2.790 3.792 + 1923WAT O 5762 3.214 1.914 3.892 + 1923WAT H1 5763 3.249 1.873 3.808 + 1923WAT H2 5764 3.124 1.876 3.912 + 1924WAT O 5765 1.901 2.939 4.024 + 1924WAT H1 5766 2.000 2.928 4.015 + 1924WAT H2 5767 1.861 2.853 4.056 + 1925WAT O 5768 2.087 3.999 0.996 + 1925WAT H1 5769 2.122 3.982 1.088 + 1925WAT H2 5770 1.999 3.954 0.984 + 1926WAT O 5771 1.881 4.092 0.647 + 1926WAT H1 5772 1.799 4.135 0.686 + 1926WAT H2 5773 1.853 4.019 0.584 + 1927WAT O 5774 2.300 4.116 1.499 + 1927WAT H1 5775 2.382 4.060 1.508 + 1927WAT H2 5776 2.219 4.058 1.503 + 1928WAT O 5777 3.456 3.838 1.480 + 1928WAT H1 5778 3.438 3.905 1.408 + 1928WAT H2 5779 3.453 3.884 1.569 + 1929WAT O 5780 2.671 3.728 0.502 + 1929WAT H1 5781 2.711 3.819 0.493 + 1929WAT H2 5782 2.571 3.736 0.508 + 1930WAT O 5783 3.143 4.069 0.944 + 1930WAT H1 5784 3.057 4.019 0.931 + 1930WAT H2 5785 3.205 4.015 1.000 + 1931WAT O 5786 2.412 3.920 0.885 + 1931WAT H1 5787 2.407 3.915 0.985 + 1931WAT H2 5788 2.414 4.016 0.856 + 1932WAT O 5789 2.064 4.009 1.498 + 1932WAT H1 5790 1.984 4.069 1.485 + 1932WAT H2 5791 2.054 3.960 1.584 + 1933WAT O 5792 3.262 3.831 0.426 + 1933WAT H1 5793 3.238 3.794 0.336 + 1933WAT H2 5794 3.361 3.847 0.430 + 1934WAT O 5795 3.409 3.946 1.729 + 1934WAT H1 5796 3.404 3.983 1.821 + 1934WAT H2 5797 3.337 3.877 1.717 + 1935WAT O 5798 2.476 3.846 0.117 + 1935WAT H1 5799 2.574 3.824 0.124 + 1935WAT H2 5800 2.445 3.829 0.024 + 1936WAT O 5801 2.643 3.988 1.749 + 1936WAT H1 5802 2.710 3.927 1.792 + 1936WAT H2 5803 2.570 4.007 1.814 + 1937WAT O 5804 2.401 3.788 0.512 + 1937WAT H1 5805 2.320 3.789 0.570 + 1937WAT H2 5806 2.404 3.871 0.457 + 1938WAT O 5807 2.423 3.946 1.147 + 1938WAT H1 5808 2.461 3.862 1.184 + 1938WAT H2 5809 2.335 3.965 1.191 + 1939WAT O 5810 2.879 3.763 0.753 + 1939WAT H1 5811 2.807 3.768 0.684 + 1939WAT H2 5812 2.855 3.694 0.822 + 1940WAT O 5813 2.777 3.813 1.402 + 1940WAT H1 5814 2.802 3.793 1.307 + 1940WAT H2 5815 2.849 3.869 1.444 + 1941WAT O 5816 3.136 4.110 1.262 + 1941WAT H1 5817 3.157 4.184 1.326 + 1941WAT H2 5818 3.047 4.127 1.219 + 1942WAT O 5819 2.366 3.774 1.740 + 1942WAT H1 5820 2.324 3.717 1.670 + 1942WAT H2 5821 2.300 3.843 1.772 + 1943WAT O 5822 2.169 3.937 1.231 + 1943WAT H1 5823 2.146 3.974 1.321 + 1943WAT H2 5824 2.139 3.842 1.225 + 1944WAT O 5825 3.402 3.998 0.125 + 1944WAT H1 5826 3.341 3.923 0.148 + 1944WAT H2 5827 3.424 4.050 0.208 + 1945WAT O 5828 3.022 3.931 1.477 + 1945WAT H1 5829 3.022 3.995 1.554 + 1945WAT H2 5830 3.050 3.979 1.394 + 1946WAT O 5831 2.765 3.810 0.133 + 1946WAT H1 5832 2.816 3.811 0.047 + 1946WAT H2 5833 2.821 3.768 0.204 + 1947WAT O 5834 3.588 3.859 0.523 + 1947WAT H1 5835 3.661 3.842 0.456 + 1947WAT H2 5836 3.557 3.772 0.561 + 1948WAT O 5837 3.703 3.899 0.963 + 1948WAT H1 5838 3.742 3.814 0.927 + 1948WAT H2 5839 3.605 3.901 0.944 + 1949WAT O 5840 2.534 3.927 1.489 + 1949WAT H1 5841 2.624 3.911 1.449 + 1949WAT H2 5842 2.542 3.932 1.588 + 1950WAT O 5843 1.934 3.890 0.318 + 1950WAT H1 5844 1.917 3.973 0.264 + 1950WAT H2 5845 2.024 3.853 0.296 + 1951WAT O 5846 3.087 4.049 0.449 + 1951WAT H1 5847 3.152 3.975 0.438 + 1951WAT H2 5848 3.107 4.099 0.533 + 1952WAT O 5849 3.639 4.066 1.642 + 1952WAT H1 5850 3.622 4.097 1.548 + 1952WAT H2 5851 3.555 4.029 1.680 + 1953WAT O 5852 3.686 3.916 1.227 + 1953WAT H1 5853 3.682 3.826 1.271 + 1953WAT H2 5854 3.689 3.905 1.128 + 1954WAT O 5855 3.286 3.938 1.112 + 1954WAT H1 5856 3.338 3.873 1.167 + 1954WAT H2 5857 3.237 4.001 1.173 + 1955WAT O 5858 2.863 3.758 1.154 + 1955WAT H1 5859 2.800 3.686 1.123 + 1955WAT H2 5860 2.956 3.722 1.154 + 1956WAT O 5861 3.214 3.776 0.168 + 1956WAT H1 5862 3.249 3.735 0.084 + 1956WAT H2 5863 3.124 3.738 0.188 + 1957WAT O 5864 3.162 4.177 0.691 + 1957WAT H1 5865 3.103 4.257 0.695 + 1957WAT H2 5866 3.177 4.142 0.784 + 1958WAT O 5867 3.455 3.945 0.882 + 1958WAT H1 5868 3.371 3.944 0.936 + 1958WAT H2 5869 3.457 4.028 0.826 + 1959WAT O 5870 2.087 3.999 2.858 + 1959WAT H1 5871 2.122 3.982 2.950 + 1959WAT H2 5872 1.999 3.954 2.846 + 1960WAT O 5873 1.881 4.092 2.509 + 1960WAT H1 5874 1.799 4.135 2.548 + 1960WAT H2 5875 1.853 4.019 2.446 + 1961WAT O 5876 3.617 4.331 2.093 + 1961WAT H1 5877 3.605 4.318 1.994 + 1961WAT H2 5878 3.587 4.250 2.142 + 1962WAT O 5879 2.300 4.116 3.361 + 1962WAT H1 5880 2.382 4.060 3.370 + 1962WAT H2 5881 2.219 4.058 3.365 + 1963WAT O 5882 3.456 3.838 3.342 + 1963WAT H1 5883 3.438 3.905 3.270 + 1963WAT H2 5884 3.453 3.884 3.431 + 1964WAT O 5885 2.671 3.728 2.364 + 1964WAT H1 5886 2.711 3.819 2.355 + 1964WAT H2 5887 2.571 3.736 2.370 + 1965WAT O 5888 3.143 4.069 2.806 + 1965WAT H1 5889 3.057 4.019 2.793 + 1965WAT H2 5890 3.205 4.015 2.862 + 1966WAT O 5891 2.412 3.920 2.747 + 1966WAT H1 5892 2.407 3.915 2.847 + 1966WAT H2 5893 2.414 4.016 2.718 + 1967WAT O 5894 2.064 4.009 3.360 + 1967WAT H1 5895 1.984 4.069 3.347 + 1967WAT H2 5896 2.054 3.960 3.446 + 1968WAT O 5897 3.262 3.831 2.288 + 1968WAT H1 5898 3.238 3.794 2.198 + 1968WAT H2 5899 3.361 3.847 2.292 + 1969WAT O 5900 3.409 3.946 3.591 + 1969WAT H1 5901 3.404 3.983 3.683 + 1969WAT H2 5902 3.337 3.877 3.579 + 1970WAT O 5903 2.476 3.846 1.979 + 1970WAT H1 5904 2.574 3.824 1.986 + 1970WAT H2 5905 2.445 3.829 1.886 + 1971WAT O 5906 2.643 3.988 3.611 + 1971WAT H1 5907 2.710 3.927 3.654 + 1971WAT H2 5908 2.570 4.007 3.676 + 1972WAT O 5909 2.401 3.788 2.374 + 1972WAT H1 5910 2.320 3.789 2.432 + 1972WAT H2 5911 2.404 3.871 2.319 + 1973WAT O 5912 2.159 3.759 2.033 + 1973WAT H1 5913 2.208 3.843 2.012 + 1973WAT H2 5914 2.221 3.694 2.078 + 1974WAT O 5915 2.423 3.946 3.009 + 1974WAT H1 5916 2.461 3.862 3.046 + 1974WAT H2 5917 2.335 3.965 3.053 + 1975WAT O 5918 2.879 3.763 2.615 + 1975WAT H1 5919 2.807 3.768 2.546 + 1975WAT H2 5920 2.855 3.694 2.684 + 1976WAT O 5921 2.777 3.813 3.264 + 1976WAT H1 5922 2.802 3.793 3.169 + 1976WAT H2 5923 2.849 3.869 3.306 + 1977WAT O 5924 3.136 4.110 3.124 + 1977WAT H1 5925 3.157 4.184 3.188 + 1977WAT H2 5926 3.047 4.127 3.081 + 1978WAT O 5927 2.366 3.774 3.602 + 1978WAT H1 5928 2.324 3.717 3.532 + 1978WAT H2 5929 2.300 3.843 3.634 + 1979WAT O 5930 2.169 3.937 3.093 + 1979WAT H1 5931 2.146 3.974 3.183 + 1979WAT H2 5932 2.139 3.842 3.087 + 1980WAT O 5933 3.402 3.998 1.987 + 1980WAT H1 5934 3.341 3.923 2.010 + 1980WAT H2 5935 3.424 4.050 2.070 + 1981WAT O 5936 3.022 3.931 3.339 + 1981WAT H1 5937 3.022 3.995 3.416 + 1981WAT H2 5938 3.050 3.979 3.256 + 1982WAT O 5939 2.765 3.810 1.995 + 1982WAT H1 5940 2.816 3.811 1.909 + 1982WAT H2 5941 2.821 3.768 2.066 + 1983WAT O 5942 3.588 3.859 2.385 + 1983WAT H1 5943 3.661 3.842 2.318 + 1983WAT H2 5944 3.557 3.772 2.423 + 1984WAT O 5945 3.703 3.899 2.825 + 1984WAT H1 5946 3.742 3.814 2.789 + 1984WAT H2 5947 3.605 3.901 2.806 + 1985WAT O 5948 2.534 3.927 3.351 + 1985WAT H1 5949 2.624 3.911 3.311 + 1985WAT H2 5950 2.542 3.932 3.450 + 1986WAT O 5951 1.937 4.069 1.895 + 1986WAT H1 5952 1.845 4.041 1.866 + 1986WAT H2 5953 1.968 4.146 1.839 + 1987WAT O 5954 1.934 3.890 2.180 + 1987WAT H1 5955 1.917 3.973 2.126 + 1987WAT H2 5956 2.024 3.853 2.158 + 1988WAT O 5957 3.087 4.049 2.311 + 1988WAT H1 5958 3.152 3.975 2.300 + 1988WAT H2 5959 3.107 4.099 2.395 + 1989WAT O 5960 3.639 4.066 3.504 + 1989WAT H1 5961 3.622 4.097 3.410 + 1989WAT H2 5962 3.555 4.029 3.542 + 1990WAT O 5963 3.686 3.916 3.089 + 1990WAT H1 5964 3.682 3.826 3.133 + 1990WAT H2 5965 3.689 3.905 2.990 + 1991WAT O 5966 3.286 3.938 2.974 + 1991WAT H1 5967 3.338 3.873 3.029 + 1991WAT H2 5968 3.237 4.001 3.035 + 1992WAT O 5969 2.863 3.758 3.016 + 1992WAT H1 5970 2.800 3.686 2.985 + 1992WAT H2 5971 2.956 3.722 3.016 + 1993WAT O 5972 3.214 3.776 2.030 + 1993WAT H1 5973 3.249 3.735 1.946 + 1993WAT H2 5974 3.124 3.738 2.050 + 1994WAT O 5975 3.162 4.177 2.553 + 1994WAT H1 5976 3.103 4.257 2.557 + 1994WAT H2 5977 3.177 4.142 2.646 + 1995WAT O 5978 3.455 3.945 2.744 + 1995WAT H1 5979 3.371 3.944 2.798 + 1995WAT H2 5980 3.457 4.028 2.688 + 1996WAT O 5981 3.617 4.331 3.955 + 1996WAT H1 5982 3.605 4.318 3.856 + 1996WAT H2 5983 3.587 4.250 4.004 + 1997WAT O 5984 2.476 3.846 3.841 + 1997WAT H1 5985 2.574 3.824 3.848 + 1997WAT H2 5986 2.445 3.829 3.748 + 1998WAT O 5987 2.159 3.759 3.895 + 1998WAT H1 5988 2.208 3.843 3.874 + 1998WAT H2 5989 2.221 3.694 3.940 + 1999WAT O 5990 3.071 4.249 3.999 + 1999WAT H1 5991 3.084 4.165 4.053 + 1999WAT H2 5992 3.042 4.323 4.059 + 2000WAT O 5993 3.402 3.998 3.849 + 2000WAT H1 5994 3.341 3.923 3.872 + 2000WAT H2 5995 3.424 4.050 3.932 + 2001WAT O 5996 2.335 4.224 3.915 + 2001WAT H1 5997 2.396 4.304 3.919 + 2001WAT H2 5998 2.240 4.255 3.922 + 2002WAT O 5999 3.588 3.859 4.247 + 2002WAT H1 6000 3.661 3.842 4.180 + 2002WAT H2 6001 3.557 3.772 4.285 + 2003WAT O 6002 1.937 4.069 3.757 + 2003WAT H1 6003 1.845 4.041 3.728 + 2003WAT H2 6004 1.968 4.146 3.701 + 2004WAT O 6005 1.934 3.890 4.042 + 2004WAT H1 6006 1.917 3.973 3.988 + 2004WAT H2 6007 2.024 3.853 4.020 + 2005WAT O 6008 3.214 3.776 3.892 + 2005WAT H1 6009 3.249 3.735 3.808 + 2005WAT H2 6010 3.124 3.738 3.912 + 2006WAT O 6011 3.954 0.628 0.113 + 2006WAT H1 6012 3.861 0.626 0.150 + 2006WAT H2 6013 3.955 0.589 0.021 + 2007WAT O 6014 3.949 0.275 0.996 + 2007WAT H1 6015 3.984 0.258 1.088 + 2007WAT H2 6016 3.861 0.230 0.984 + 2008WAT O 6017 3.743 0.368 0.647 + 2008WAT H1 6018 3.661 0.411 0.686 + 2008WAT H2 6019 3.715 0.295 0.584 + 2009WAT O 6020 4.059 1.435 1.061 + 2009WAT H1 6021 3.981 1.404 1.008 + 2009WAT H2 6022 4.117 1.493 1.004 + 2010WAT O 6023 3.955 1.713 0.483 + 2010WAT H1 6024 3.989 1.790 0.537 + 2010WAT H2 6025 3.999 1.713 0.393 + 2011WAT O 6026 3.954 1.434 0.538 + 2011WAT H1 6027 3.928 1.530 0.538 + 2011WAT H2 6028 3.883 1.380 0.583 + 2012WAT O 6029 3.846 0.643 0.563 + 2012WAT H1 6030 3.801 0.555 0.580 + 2012WAT H2 6031 3.845 0.697 0.647 + 2013WAT O 6032 3.751 1.596 0.117 + 2013WAT H1 6033 3.732 1.500 0.138 + 2013WAT H2 6034 3.718 1.654 0.192 + 2014WAT O 6035 3.837 0.737 1.597 + 2014WAT H1 6036 3.925 0.724 1.642 + 2014WAT H2 6037 3.824 0.834 1.575 + 2015WAT O 6038 3.800 0.811 0.789 + 2015WAT H1 6039 3.899 0.799 0.798 + 2015WAT H2 6040 3.776 0.906 0.810 + 2016WAT O 6041 3.854 1.821 1.571 + 2016WAT H1 6042 3.844 1.806 1.670 + 2016WAT H2 6043 3.768 1.857 1.535 + 2017WAT O 6044 3.926 0.285 1.498 + 2017WAT H1 6045 3.846 0.345 1.485 + 2017WAT H2 6046 3.916 0.236 1.584 + 2018WAT O 6047 3.802 0.556 1.386 + 2018WAT H1 6048 3.894 0.555 1.345 + 2018WAT H2 6049 3.796 0.630 1.453 + 2019WAT O 6050 4.251 0.256 0.328 + 2019WAT H1 6051 4.278 0.197 0.253 + 2019WAT H2 6052 4.251 0.351 0.297 + 2020WAT O 6053 3.788 1.564 1.331 + 2020WAT H1 6054 3.742 1.646 1.297 + 2020WAT H2 6055 3.886 1.583 1.340 + 2021WAT O 6056 4.091 1.100 0.501 + 2021WAT H1 6057 4.084 1.183 0.445 + 2021WAT H2 6058 4.095 1.020 0.441 + 2022WAT O 6059 4.031 0.213 1.231 + 2022WAT H1 6060 4.008 0.250 1.321 + 2022WAT H2 6061 4.001 0.118 1.225 + 2023WAT O 6062 3.761 1.310 1.282 + 2023WAT H1 6063 3.814 1.261 1.350 + 2023WAT H2 6064 3.783 1.408 1.287 + 2024WAT O 6065 3.732 1.326 0.200 + 2024WAT H1 6066 3.639 1.347 0.169 + 2024WAT H2 6067 3.742 1.227 0.213 + 2025WAT O 6068 3.812 1.801 0.927 + 2025WAT H1 6069 3.770 1.715 0.900 + 2025WAT H2 6070 3.906 1.804 0.893 + 2026WAT O 6071 4.228 1.568 0.910 + 2026WAT H1 6072 4.294 1.642 0.919 + 2026WAT H2 6073 4.272 1.489 0.868 + 2027WAT O 6074 3.764 0.544 1.114 + 2027WAT H1 6075 3.849 0.511 1.073 + 2027WAT H2 6076 3.777 0.559 1.212 + 2028WAT O 6077 3.913 0.520 1.722 + 2028WAT H1 6078 3.972 0.480 1.652 + 2028WAT H2 6079 3.855 0.591 1.681 + 2029WAT O 6080 3.976 1.564 1.744 + 2029WAT H1 6081 3.946 1.621 1.820 + 2029WAT H2 6082 3.969 1.467 1.770 + 2030WAT O 6083 3.883 1.137 1.466 + 2030WAT H1 6084 3.905 1.076 1.542 + 2030WAT H2 6085 3.893 1.088 1.380 + 2031WAT O 6086 3.807 1.258 1.022 + 2031WAT H1 6087 3.802 1.257 1.122 + 2031WAT H2 6088 3.724 1.217 0.984 + 2032WAT O 6089 3.854 1.794 1.851 + 2032WAT H1 6090 3.813 1.720 1.904 + 2032WAT H2 6091 3.918 1.845 1.909 + 2033WAT O 6092 3.796 0.166 0.318 + 2033WAT H1 6093 3.779 0.249 0.264 + 2033WAT H2 6094 3.886 0.129 0.296 + 2034WAT O 6095 3.803 1.240 0.653 + 2034WAT H1 6096 3.802 1.193 0.741 + 2034WAT H2 6097 3.885 1.212 0.602 + 2035WAT O 6098 3.763 1.077 0.300 + 2035WAT H1 6099 3.862 1.066 0.291 + 2035WAT H2 6100 3.723 0.991 0.332 + 2036WAT O 6101 3.954 0.628 1.975 + 2036WAT H1 6102 3.861 0.626 2.012 + 2036WAT H2 6103 3.955 0.589 1.883 + 2037WAT O 6104 3.949 0.275 2.858 + 2037WAT H1 6105 3.984 0.258 2.950 + 2037WAT H2 6106 3.861 0.230 2.846 + 2038WAT O 6107 3.743 0.368 2.509 + 2038WAT H1 6108 3.661 0.411 2.548 + 2038WAT H2 6109 3.715 0.295 2.446 + 2039WAT O 6110 4.059 1.435 2.923 + 2039WAT H1 6111 3.981 1.404 2.870 + 2039WAT H2 6112 4.117 1.493 2.866 + 2040WAT O 6113 3.955 1.713 2.345 + 2040WAT H1 6114 3.989 1.790 2.399 + 2040WAT H2 6115 3.999 1.713 2.255 + 2041WAT O 6116 3.954 1.434 2.400 + 2041WAT H1 6117 3.928 1.530 2.400 + 2041WAT H2 6118 3.883 1.380 2.445 + 2042WAT O 6119 3.846 0.643 2.425 + 2042WAT H1 6120 3.801 0.555 2.442 + 2042WAT H2 6121 3.845 0.697 2.509 + 2043WAT O 6122 3.751 1.596 1.979 + 2043WAT H1 6123 3.732 1.500 2.000 + 2043WAT H2 6124 3.718 1.654 2.054 + 2044WAT O 6125 3.837 0.737 3.459 + 2044WAT H1 6126 3.925 0.724 3.504 + 2044WAT H2 6127 3.824 0.834 3.437 + 2045WAT O 6128 3.800 0.811 2.651 + 2045WAT H1 6129 3.899 0.799 2.660 + 2045WAT H2 6130 3.776 0.906 2.672 + 2046WAT O 6131 3.854 1.821 3.433 + 2046WAT H1 6132 3.844 1.806 3.532 + 2046WAT H2 6133 3.768 1.857 3.397 + 2047WAT O 6134 3.926 0.285 3.360 + 2047WAT H1 6135 3.846 0.345 3.347 + 2047WAT H2 6136 3.916 0.236 3.446 + 2048WAT O 6137 3.802 0.556 3.248 + 2048WAT H1 6138 3.894 0.555 3.207 + 2048WAT H2 6139 3.796 0.630 3.315 + 2049WAT O 6140 4.251 0.256 2.190 + 2049WAT H1 6141 4.278 0.197 2.115 + 2049WAT H2 6142 4.251 0.351 2.159 + 2050WAT O 6143 3.788 1.564 3.193 + 2050WAT H1 6144 3.742 1.646 3.159 + 2050WAT H2 6145 3.886 1.583 3.202 + 2051WAT O 6146 4.091 1.100 2.363 + 2051WAT H1 6147 4.084 1.183 2.307 + 2051WAT H2 6148 4.095 1.020 2.303 + 2052WAT O 6149 4.031 0.213 3.093 + 2052WAT H1 6150 4.008 0.250 3.183 + 2052WAT H2 6151 4.001 0.118 3.087 + 2053WAT O 6152 3.761 1.310 3.144 + 2053WAT H1 6153 3.814 1.261 3.212 + 2053WAT H2 6154 3.783 1.408 3.149 + 2054WAT O 6155 3.732 1.326 2.062 + 2054WAT H1 6156 3.639 1.347 2.031 + 2054WAT H2 6157 3.742 1.227 2.075 + 2055WAT O 6158 3.812 1.801 2.789 + 2055WAT H1 6159 3.770 1.715 2.762 + 2055WAT H2 6160 3.906 1.804 2.755 + 2056WAT O 6161 4.228 1.568 2.772 + 2056WAT H1 6162 4.294 1.642 2.781 + 2056WAT H2 6163 4.272 1.489 2.730 + 2057WAT O 6164 3.764 0.544 2.976 + 2057WAT H1 6165 3.849 0.511 2.935 + 2057WAT H2 6166 3.777 0.559 3.074 + 2058WAT O 6167 3.913 0.520 3.584 + 2058WAT H1 6168 3.972 0.480 3.514 + 2058WAT H2 6169 3.855 0.591 3.543 + 2059WAT O 6170 3.976 1.564 3.606 + 2059WAT H1 6171 3.946 1.621 3.682 + 2059WAT H2 6172 3.969 1.467 3.632 + 2060WAT O 6173 3.883 1.137 3.328 + 2060WAT H1 6174 3.905 1.076 3.404 + 2060WAT H2 6175 3.893 1.088 3.242 + 2061WAT O 6176 3.807 1.258 2.884 + 2061WAT H1 6177 3.802 1.257 2.984 + 2061WAT H2 6178 3.724 1.217 2.846 + 2062WAT O 6179 3.854 1.794 3.713 + 2062WAT H1 6180 3.813 1.720 3.766 + 2062WAT H2 6181 3.918 1.845 3.771 + 2063WAT O 6182 3.799 0.345 1.895 + 2063WAT H1 6183 3.707 0.317 1.866 + 2063WAT H2 6184 3.830 0.422 1.839 + 2064WAT O 6185 3.796 0.166 2.180 + 2064WAT H1 6186 3.779 0.249 2.126 + 2064WAT H2 6187 3.886 0.129 2.158 + 2065WAT O 6188 3.803 1.240 2.515 + 2065WAT H1 6189 3.802 1.193 2.603 + 2065WAT H2 6190 3.885 1.212 2.464 + 2066WAT O 6191 3.763 1.077 2.162 + 2066WAT H1 6192 3.862 1.066 2.153 + 2066WAT H2 6193 3.723 0.991 2.194 + 2067WAT O 6194 3.954 0.628 3.837 + 2067WAT H1 6195 3.861 0.626 3.874 + 2067WAT H2 6196 3.955 0.589 3.745 + 2068WAT O 6197 3.751 1.596 3.841 + 2068WAT H1 6198 3.732 1.500 3.862 + 2068WAT H2 6199 3.718 1.654 3.916 + 2069WAT O 6200 3.732 1.326 3.924 + 2069WAT H1 6201 3.639 1.347 3.893 + 2069WAT H2 6202 3.742 1.227 3.937 + 2070WAT O 6203 3.799 0.345 3.757 + 2070WAT H1 6204 3.707 0.317 3.728 + 2070WAT H2 6205 3.830 0.422 3.701 + 2071WAT O 6206 3.763 1.077 4.024 + 2071WAT H1 6207 3.862 1.066 4.015 + 2071WAT H2 6208 3.723 0.991 4.056 + 2072WAT O 6209 3.954 2.490 0.113 + 2072WAT H1 6210 3.861 2.488 0.150 + 2072WAT H2 6211 3.955 2.451 0.021 + 2073WAT O 6212 3.949 2.137 0.996 + 2073WAT H1 6213 3.984 2.120 1.088 + 2073WAT H2 6214 3.861 2.092 0.984 + 2074WAT O 6215 3.743 2.230 0.647 + 2074WAT H1 6216 3.661 2.273 0.686 + 2074WAT H2 6217 3.715 2.157 0.584 + 2075WAT O 6218 4.059 3.297 1.061 + 2075WAT H1 6219 3.981 3.266 1.008 + 2075WAT H2 6220 4.117 3.355 1.004 + 2076WAT O 6221 3.955 3.575 0.483 + 2076WAT H1 6222 3.989 3.652 0.537 + 2076WAT H2 6223 3.999 3.575 0.393 + 2077WAT O 6224 3.954 3.296 0.538 + 2077WAT H1 6225 3.928 3.392 0.538 + 2077WAT H2 6226 3.883 3.242 0.583 + 2078WAT O 6227 3.846 2.505 0.563 + 2078WAT H1 6228 3.801 2.417 0.580 + 2078WAT H2 6229 3.845 2.559 0.647 + 2079WAT O 6230 3.751 3.458 0.117 + 2079WAT H1 6231 3.732 3.362 0.138 + 2079WAT H2 6232 3.718 3.516 0.192 + 2080WAT O 6233 3.837 2.599 1.597 + 2080WAT H1 6234 3.925 2.586 1.642 + 2080WAT H2 6235 3.824 2.696 1.575 + 2081WAT O 6236 3.800 2.673 0.789 + 2081WAT H1 6237 3.899 2.661 0.798 + 2081WAT H2 6238 3.776 2.768 0.810 + 2082WAT O 6239 3.854 3.683 1.571 + 2082WAT H1 6240 3.844 3.668 1.670 + 2082WAT H2 6241 3.768 3.719 1.535 + 2083WAT O 6242 3.926 2.147 1.498 + 2083WAT H1 6243 3.846 2.207 1.485 + 2083WAT H2 6244 3.916 2.098 1.584 + 2084WAT O 6245 4.021 1.897 0.171 + 2084WAT H1 6246 4.070 1.981 0.150 + 2084WAT H2 6247 4.083 1.832 0.216 + 2085WAT O 6248 3.802 2.418 1.386 + 2085WAT H1 6249 3.894 2.417 1.345 + 2085WAT H2 6250 3.796 2.492 1.453 + 2086WAT O 6251 4.251 2.118 0.328 + 2086WAT H1 6252 4.278 2.059 0.253 + 2086WAT H2 6253 4.251 2.213 0.297 + 2087WAT O 6254 3.788 3.426 1.331 + 2087WAT H1 6255 3.742 3.508 1.297 + 2087WAT H2 6256 3.886 3.445 1.340 + 2088WAT O 6257 4.091 2.962 0.501 + 2088WAT H1 6258 4.084 3.045 0.445 + 2088WAT H2 6259 4.095 2.882 0.441 + 2089WAT O 6260 4.031 2.075 1.231 + 2089WAT H1 6261 4.008 2.112 1.321 + 2089WAT H2 6262 4.001 1.980 1.225 + 2090WAT O 6263 3.761 3.172 1.282 + 2090WAT H1 6264 3.814 3.123 1.350 + 2090WAT H2 6265 3.783 3.270 1.287 + 2091WAT O 6266 4.031 1.925 0.618 + 2091WAT H1 6267 4.020 2.019 0.651 + 2091WAT H2 6268 4.026 1.862 0.695 + 2092WAT O 6269 3.732 3.188 0.200 + 2092WAT H1 6270 3.639 3.209 0.169 + 2092WAT H2 6271 3.742 3.089 0.213 + 2093WAT O 6272 3.812 3.663 0.927 + 2093WAT H1 6273 3.770 3.577 0.900 + 2093WAT H2 6274 3.906 3.666 0.893 + 2094WAT O 6275 4.228 3.430 0.910 + 2094WAT H1 6276 4.294 3.504 0.919 + 2094WAT H2 6277 4.272 3.351 0.868 + 2095WAT O 6278 3.764 2.406 1.114 + 2095WAT H1 6279 3.849 2.373 1.073 + 2095WAT H2 6280 3.777 2.421 1.212 + 2096WAT O 6281 3.913 2.382 1.722 + 2096WAT H1 6282 3.972 2.342 1.652 + 2096WAT H2 6283 3.855 2.453 1.681 + 2097WAT O 6284 3.976 3.426 1.744 + 2097WAT H1 6285 3.946 3.483 1.820 + 2097WAT H2 6286 3.969 3.329 1.770 + 2098WAT O 6287 3.883 2.999 1.466 + 2098WAT H1 6288 3.905 2.938 1.542 + 2098WAT H2 6289 3.893 2.950 1.380 + 2099WAT O 6290 3.807 3.120 1.022 + 2099WAT H1 6291 3.802 3.119 1.122 + 2099WAT H2 6292 3.724 3.079 0.984 + 2100WAT O 6293 3.854 3.656 1.851 + 2100WAT H1 6294 3.813 3.582 1.904 + 2100WAT H2 6295 3.918 3.707 1.909 + 2101WAT O 6296 3.799 2.207 0.033 + 2101WAT H1 6297 3.707 2.179 0.004 + 2101WAT H2 6298 3.830 2.284 -0.023 + 2102WAT O 6299 3.796 2.028 0.318 + 2102WAT H1 6300 3.779 2.111 0.264 + 2102WAT H2 6301 3.886 1.991 0.296 + 2103WAT O 6302 3.803 3.102 0.653 + 2103WAT H1 6303 3.802 3.055 0.741 + 2103WAT H2 6304 3.885 3.074 0.602 + 2104WAT O 6305 3.763 2.939 0.300 + 2104WAT H1 6306 3.862 2.928 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alchemical_run/test-data/morph.top Mon Nov 11 13:20:39 2019 -0500 @@ -0,0 +1,232 @@ +; Gromacs Topology File written by Sire +; File written 05/01/19 13:21:14 +[ defaults ] +; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ + 1 2 yes 0.5 0.833333 + +[ atomtypes ] +; name at.num mass charge ptype sigma epsilon + Cl- 17 35.453000 0.000000 A 0.447766 0.148913 + HW 1 1.007940 0.000000 A 0.000000 0.000000 + Na+ 11 22.989770 0.000000 A 0.243928 0.365846 + OW 8 15.999400 0.000000 A 0.315075 0.635968 + c3 6 12.010700 0.000000 A 0.339771 0.451035 + ca 6 12.010700 0.000000 A 0.331521 0.413379 + ha 1 1.007940 0.000000 A 0.262548 0.067362 + hc 1 1.007940 0.000000 A 0.260018 0.087027 + hc_du 0 0.000000 0.000000 A 0.000000 0.000000 + +[ moleculetype ] +; name nrexcl +CL 3 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass + 1 Cl- 1 CL CL 1 -1.000000 35.450000 + + +[ moleculetype ] +; name nrexcl +Merged_Molecule 3 + +[ atoms ] +; nr type0 resnr residue atom cgnr charge0 mass0 type1 charge1 mass1 + 1 ca 1 LIG C 1 -0.130000 12.010000 ca -0.075744 12.010000 + 2 ca 1 LIG C1 2 -0.130000 12.010000 ca -0.129444 12.010000 + 3 ca 1 LIG C2 3 -0.130000 12.010000 ca -0.131444 12.010000 + 4 ca 1 LIG C3 4 -0.130000 12.010000 ca -0.131444 12.010000 + 5 ca 1 LIG C4 5 -0.130000 12.010000 ca -0.129444 12.010000 + 6 ca 1 LIG C5 6 -0.130000 12.010000 ca -0.075744 12.010000 + 7 ha 1 LIG H 7 0.130000 1.008000 c3 -0.053744 12.010000 + 8 ha 1 LIG H1 8 0.130000 1.008000 ha 0.129056 1.008000 + 9 ha 1 LIG H2 9 0.130000 1.008000 ha 0.130056 1.008000 + 10 ha 1 LIG H3 10 0.130000 1.008000 ha 0.130056 1.008000 + 11 ha 1 LIG H4 11 0.130000 1.008000 ha 0.129056 1.008000 + 12 ha 1 LIG H5 12 0.130000 1.008000 c3 -0.053744 12.010000 + 13 hc_du 1 LIG H 13 0.000000 1.008000 hc 0.043756 1.008000 + 14 hc_du 1 LIG H1 14 0.000000 1.008000 hc 0.043756 1.008000 + 15 hc_du 1 LIG H2 15 0.000000 1.008000 hc 0.043756 1.008000 + 16 hc_du 1 LIG H7 16 0.000000 1.008000 hc 0.043756 1.008000 + 17 hc_du 1 LIG H8 17 0.000000 1.008000 hc 0.043756 1.008000 + 18 hc_du 1 LIG H9 18 0.000000 1.008000 hc 0.043756 1.008000 + +[ bonds ] +; ai aj funct parameters + 1 2 1 0.1398 316812 0.1398 316812 + 1 6 1 0.1398 316812 0.1398 316812 + 1 7 1 0.1086 331122 0.1516 209451 + 2 3 1 0.1398 316812 0.1398 316812 + 2 8 1 0.1086 331122 0.1086 331122 + 3 4 1 0.1398 316812 0.1398 316812 + 3 9 1 0.1086 331122 0.1086 331122 + 4 5 1 0.1398 316812 0.1398 316812 + 4 10 1 0.1086 331122 0.1086 331122 + 5 6 1 0.1398 316812 0.1398 316812 + 5 11 1 0.1086 331122 0.1086 331122 + 6 12 1 0.1086 331122 0.1516 209451 + 7 13 1 0.1097 314553 0.1097 314553 + 7 14 1 0.1097 314553 0.1097 314553 + 7 15 1 0.1097 314553 0.1097 314553 + 12 16 1 0.1097 314553 0.1097 314553 + 12 17 1 0.1097 314553 0.1097 314553 + 12 18 1 0.1097 314553 0.1097 314553 + +[ pairs ] +; ai aj funct + 1 4 1 + 1 9 1 + 1 11 1 + 1 16 1 + 1 17 1 + 1 18 1 + 2 5 1 + 2 10 1 + 2 12 1 + 2 13 1 + 2 14 1 + 2 15 1 + 3 6 1 + 3 7 1 + 3 11 1 + 4 8 1 + 4 12 1 + 5 7 1 + 5 9 1 + 5 16 1 + 5 17 1 + 5 18 1 + 6 8 1 + 6 10 1 + 6 13 1 + 6 14 1 + 6 15 1 + 7 8 1 + 7 12 1 + 8 9 1 + 9 10 1 + 10 11 1 + 11 12 1 + +[ angles ] +; ai aj ak funct parameters + 1 2 3 1 120.02 575.718 120.02 575.718 + 1 2 8 1 119.88 407.522 119.88 407.522 + 1 6 5 1 120.02 575.718 120.02 575.718 + 1 6 12 1 119.88 407.522 120.77 548.941 + 1 7 13 1 110.47 395.806 110.47 395.806 + 1 7 14 1 110.47 395.806 110.47 395.806 + 1 7 15 1 110.47 395.806 110.47 395.806 + 2 1 6 1 120.02 575.718 120.02 575.718 + 2 1 7 1 119.88 407.522 120.77 548.941 + 2 3 4 1 120.02 575.718 120.02 575.718 + 2 3 9 1 119.88 407.522 119.88 407.522 + 3 2 8 1 119.88 407.522 119.88 407.522 + 3 4 5 1 120.02 575.718 120.02 575.718 + 3 4 10 1 119.88 407.522 119.88 407.522 + 4 3 9 1 119.88 407.522 119.88 407.522 + 4 5 6 1 120.02 575.718 120.02 575.718 + 4 5 11 1 119.88 407.522 119.88 407.522 + 5 4 10 1 119.88 407.522 119.88 407.522 + 5 6 12 1 119.88 407.522 120.77 548.941 + 6 1 7 1 119.88 407.522 120.77 548.941 + 6 5 11 1 119.88 407.522 119.88 407.522 + 6 12 16 1 110.47 395.806 110.47 395.806 + 6 12 17 1 110.47 395.806 110.47 395.806 + 6 12 18 1 110.47 395.806 110.47 395.806 + 13 7 14 1 107.58 326.352 107.58 326.352 + 13 7 15 1 107.58 326.352 107.58 326.352 + 14 7 15 1 107.58 326.352 107.58 326.352 + 16 12 17 1 107.58 326.352 107.58 326.352 + 16 12 18 1 107.58 326.352 107.58 326.352 + 17 12 18 1 107.58 326.352 107.58 326.352 + +[ dihedrals ] +; ai aj ak al funct parameters + 1 2 3 4 1 180 15.167 2 180 15.167 2 + 1 2 3 9 1 180 15.167 2 180 15.167 2 + 1 3 2 8 4 180 4.6024 2 180 4.6024 2 + 1 5 6 12 4 180 4.6024 2 0 0 2 + 1 6 5 4 1 180 15.167 2 180 15.167 2 + 1 6 5 11 1 180 15.167 2 180 15.167 2 + 1 6 12 16 1 0 0 0 0 0 0 + 1 6 12 17 1 0 0 0 0 0 0 + 1 6 12 18 1 0 0 0 0 0 0 + 2 1 6 5 1 180 15.167 2 180 15.167 2 + 2 1 6 12 1 180 15.167 2 180 15.167 2 + 2 1 7 13 1 0 0 0 0 0 0 + 2 1 7 14 1 0 0 0 0 0 0 + 2 1 7 15 1 0 0 0 0 0 0 + 2 3 4 5 1 180 15.167 2 180 15.167 2 + 2 3 4 10 1 180 15.167 2 180 15.167 2 + 2 4 3 9 4 180 4.6024 2 180 4.6024 2 + 2 6 1 7 4 180 4.6024 2 180 4.6024 2 + 3 2 1 6 1 180 15.167 2 180 15.167 2 + 3 2 1 7 1 180 15.167 2 180 15.167 2 + 3 4 5 6 1 180 15.167 2 180 15.167 2 + 3 4 5 11 1 180 15.167 2 180 15.167 2 + 3 5 4 10 4 180 4.6024 2 180 4.6024 2 + 4 3 2 8 1 180 15.167 2 180 15.167 2 + 4 5 6 12 1 180 15.167 2 180 15.167 2 + 4 6 5 11 4 180 4.6024 2 180 4.6024 2 + 5 4 3 9 1 180 15.167 2 180 15.167 2 + 5 6 1 7 1 180 15.167 2 180 15.167 2 + 5 6 1 12 4 0 0 2 180 4.6024 2 + 5 6 12 16 1 0 0 0 0 0 0 + 5 6 12 17 1 0 0 0 0 0 0 + 5 6 12 18 1 0 0 0 0 0 0 + 6 1 2 8 1 180 15.167 2 180 15.167 2 + 6 1 7 13 1 0 0 0 0 0 0 + 6 1 7 14 1 0 0 0 0 0 0 + 6 1 7 15 1 0 0 0 0 0 0 + 6 5 4 10 1 180 15.167 2 180 15.167 2 + 7 1 2 8 1 180 15.167 2 180 15.167 2 + 7 1 6 12 1 180 15.167 2 180 15.167 2 + 8 2 3 9 1 180 15.167 2 180 15.167 2 + 9 3 4 10 1 180 15.167 2 180 15.167 2 + 10 4 5 11 1 180 15.167 2 180 15.167 2 + 11 5 6 12 1 180 15.167 2 180 15.167 2 + + +[ moleculetype ] +; name nrexcl +NA 3 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass + 1 Na+ 1 NA NA 1 1.000000 22.990000 + + +[ moleculetype ] +; name nrexcl +WAT 3 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass + 1 OW 1 WAT O 1 -0.834000 16.000000 + 2 HW 1 WAT H1 2 0.417000 1.008000 + 3 HW 1 WAT H2 3 0.417000 1.008000 + +#ifdef FLEXIBLE +#else + +[ settles ] +; OW funct doh dhh +1 1 0.09572 0.15136 + +[ exclusions ] +1 2 3 +2 1 3 +3 1 2 + +#endif + +[ system ] +BioSimSpace System + +[ molecules ] +;molecule name nr. +Merged_Molecule 1 + NA 5 + CL 5 + WAT 2151 +