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annotate test-data/npt.mdp @ 0:bb0053c4e4f2 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
author chemteam
date Tue, 21 Jan 2020 07:29:43 -0500
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bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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diff changeset
1 title = OPLS Lysozyme NPT equilibration
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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2 define = -DPOSRES ; position restrain the protein
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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3 ; Run parameters
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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4 integrator = md ; leap-frog integrator
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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5 nsteps = 500 ; 2 * 50000 = 100 ps
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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6 dt = 0.002 ; 2 fs
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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7 ; Output control
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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8 nstxout = 50 ; save coordinates every 1.0 ps
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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9 nstvout = 50 ; save velocities every 1.0 ps
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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10 nstenergy = 50 ; save energies every 1.0 ps
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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11 nstlog = 50 ; update log file every 1.0 ps
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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12 nstxout-compressed = 50 ; save compressed coordinates every 10.0 ps
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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13 ; Bond parameters
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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14 continuation = yes ; Restarting after NVT
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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15 constraint_algorithm = lincs ; holonomic constraints
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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16 constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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17 lincs_iter = 1 ; accuracy of LINCS
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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18 lincs_order = 4 ; also related to accuracy
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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19 ; Neighborsearching
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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20 cutoff-scheme = Verlet
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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21 ns_type = grid ; search neighboring grid cells
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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22 nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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23 rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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24 rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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25 ; Electrostatics
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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26 coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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27 pme_order = 4 ; cubic interpolation
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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28 fourierspacing = 0.16 ; grid spacing for FFT
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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29 ; Temperature coupling is on
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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30 tcoupl = V-rescale ; modified Berendsen thermostat
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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31 tc-grps = Protein Non-Protein ; two coupling groups - more accurate
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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32 tau_t = 0.1 0.1 ; time constant, in ps
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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33 ref_t = 300 300 ; reference temperature, one for each group, in K
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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34 ; Pressure coupling is on
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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35 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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36 pcoupltype = isotropic ; uniform scaling of box vectors
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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37 tau_p = 2.0 ; time constant, in ps
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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38 ref_p = 1.0 ; reference pressure, in bar
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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39 compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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40 refcoord_scaling = com
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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41 ; Periodic boundary conditions
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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42 pbc = xyz ; 3-D PBC
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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43 ; Dispersion correction
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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44 DispCorr = EnerPres ; account for cut-off vdW scheme
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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45 ; Velocity generation
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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46 gen_vel = no ; Velocity generation is off