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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author | chemteam |
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date | Mon, 07 Oct 2019 12:48:44 -0400 |
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children | ec3f665cca3e |
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<tool id="gmx_sim" name="GROMACS simulation" version="@VERSION@"> <description>for system equilibration or data collection</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ #if $mdp.mdpfile == "custom": ln -s '$mdp.mdp_input' ./md.mdp && #end if #if $mdp.mdpfile == "default": ln -s '$md' ./md.mdp && #end if ln -s '$gro_input' ./inp.gro && ln -s '$top_input' ./top_input.top && #if $posres.posres_bool == "true": ln -s '$posres.itp_inp' ./posres.itp && #end if #if $cpt_inp.cpt_bool == "yes": ln -s '$cpt_inp.cpt_in' ./inp.cpt && #end if gmx grompp -f ./md.mdp -c ./inp.gro #if $cpt_inp.cpt_bool == "yes": -t ./inp.cpt #end if #if $posres.posres_bool == "true": -r ./inp.gro #end if -p ./top_input.top -o outp.tpr &>> verbose.txt && gmx mdrun -deffnm outp &>> verbose.txt #if $str == 'pdb' or $str == 'both' && gmx editconf -f outp.gro -o outp.pdb &>> verbose.txt #end if && cat md.mdp &>> verbose.txt ]]></command> <configfiles> <!-- .mdp file for the gromacs simulation --> <configfile name="md"> #if $mdp.mdpfile == 'default': title = OPLS Lysozyme MD simulation ; Run parameters integrator = $mdp.integrator ; leap-frog integrator nsteps = $mdp.md_steps ; 2 * 500000 = 1000 ps (1 ns) dt = $mdp.step_length ; 2 fs ; Output control nstxout = $mdp.write_freq ; save coordinates every 10.0 ps nstvout = $mdp.write_freq ; save velocities every 10.0 ps nstenergy = $mdp.write_freq ; save energies every 10.0 ps nstlog = $mdp.write_freq ; update log file every 10.0 ps nstxout-compressed = $mdp.write_freq ; save compressed coordinates every 10.0 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System ; group(s) to write to the compressed trajectory file ; Bond parameters continuation = $cpt_inp.cpt_bool ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = $mdp.constraints ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = $mdp.cutoffscheme ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme rcoulomb = $mdp.rcoulomb ; Short-range electrostatic cut-off rlist = $mdp.rlist ; Cut-off distance for the short-range neighbor list. rvdw = $mdp.rvdw ; Short-range Van der Waals cut-off ; Electrostatics coulombtype = $mdp.coulombtype ; method for electrostatics calculations e.g. PME pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = $mdp.temperature $mdp.temperature ; reference temperature, one for each group, in K ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off #end if #if $posres.posres_bool == "true": define = -DPOSRES ; position restrain the protein refcoord_scaling = com #end if #if $ensemble == "nvt": pcoupl = no ; no pressure coupling in NVT #else: ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 #end if </configfile> </configfiles> <inputs> <param argument="gro_input" type="data" format='gro' label="GRO structure file"/> <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/> <conditional name="cpt_inp"> <param name="cpt_bool" type="select" label="Use a checkpoint (CPT) file" help="CPT file from a previous MD run"> <option value="yes">Continue simulation from a CPT file</option> <option value="no" selected="true">No CPT input</option> </param> <when value="yes"> <param argument="cpt_in" type="data" format='cpt' label="Checkpoint file"/> </when> <when value="no"/> </conditional> <param name="cpt_out" type="select" label="Produce a checkpoint (CPT) file" help="Produce CPT file for a subsequent MD run"> <option value="true">Produce CPT output</option> <option value="false" selected="true">No CPT output</option> </param> <conditional name="posres"> <param name="posres_bool" type="select" label="Apply position restraints" help="Used e.g. for equilibration of solvent around a protein" value="false"> <option value="true">Apply position restraints</option> <option value="false" selected="true">No position restraints</option> </param> <when value="true"> <param argument="itp_inp" type="data" format='itp' label="Position restraint (ITP) file"/> </when> <when value="false"/> </conditional> <param name="ensemble" label="Ensemble" type="select" help="NVT ensemble (constant number of particles, volume and temperature) or NPT ensemble (constant number of particles, pressure and temperature)"> <option value="nvt">Isothermal-isochoric ensemble (NVT)</option> <option value="npt">Isothermal-isobaric ensemble (NPT)</option> </param> <expand macro="md_inputs"/> </inputs> <outputs> <data name="output1" format="gro" from_work_dir="outp.gro"> <filter>str == 'gro' or str == 'both'</filter> </data> <data name="output2" format="pdb" from_work_dir="outp.pdb"> <filter>str == 'pdb' or str == 'both'</filter> </data> <data name="output3" format="trr" from_work_dir="outp.trr"> <filter>traj == 'trr' or traj == 'both'</filter> </data> <data name="output4" format="xtc" from_work_dir="outp.xtc"> <filter>traj == 'xtc' or traj == 'both'</filter> </data> <data name="output5" format="cpt" from_work_dir="outp.cpt"> <filter>cpt_out</filter> </data> <data name="report" format="txt" from_work_dir="verbose.txt"> <filter>capture_log</filter> </data> </outputs> <tests> <test> <param name="gro_input" value="npt.gro" /> <param name="top_input" value="topol_solv.top" /> <param name="cpt_bool" value="yes" /> <param name="cpt_in" value="npt.cpt" /> <param name="mdpfile" value="custom" /> <param name="mdp_input" value="md.mdp" /> <param name="traj" value="trr"/> <param name="str" value="gro"/> <param name="ensemble" value="npt" /> <param name="posres_bool" value="false" /> <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> </test> <test> <param name="gro_input" value="npt.gro" /> <param name="top_input" value="topol_solv.top" /> <param name="cpt_bool" value="yes" /> <param name="cpt_in" value="npt.cpt" /> <param name="traj" value="trr"/> <param name="str" value="both"/> <expand macro="test_params"/> <param name="ensemble" value="npt" /> <param name="posres_bool" value="false" /> <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> </test> <test> <param name="gro_input" value="em.gro" /> <param name="top_input" value="topol_solv.top" /> <param name="posres_bool" value="true" /> <param name="itp_inp" value="posres.itp" /> <param name="cpt_bool" value="no" /> <param name="cpt_out" value="true" /> <param name="traj" value="xtc"/> <param name="str" value="pdb"/> <param name="ensemble" value="nvt" /> <expand macro="test_params"/> <output name="output2" file="nvt.pdb" ftype="pdb" compare="sim_size"/> <output name="output4" file="nvt.xtc" ftype="xtc" compare="sim_size"/> <output name="output5" file="nvt.cpt" ftype="cpt" compare="sim_size"/> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** This tool performs a molecular dynamics simulation with GROMACS. _____ .. class:: infomark **Input** - GRO structure file. - Topology (TOP) file. A variety of other options can also be specified: - MDP parameter file to take advantage of all GROMACS features. Otherwise, choose parameters through the Galaxy interface. See the `manual`_ for more information on the options. - Accepting and producing checkpoint (CPT) input/output files, which allows sequential MD simulations, e.g. when performing NVT and NPT equilibration followed by a production simulation. - Position restraint (ITP) file, useful for equilibrating solvent around a protein. - Choice of ensemble: NVT or NPT. - Whether to return trajectory (XTC or TRR) and/or structure (GRO or PDB) files. .. _`manual`: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html _____ .. class:: infomark **Output** - Structure and/or trajectory files as specified in the input. ]]></help> <expand macro="citations" /> </tool>