Mercurial > repos > chemteam > gmx_editconf

annotate test-data/npt.mdp @ 2:004232c5336f draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1"
author chemteam
date Wed, 18 Dec 2019 15:25:03 -0500
parents 7b23265126b0
children
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7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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diff changeset
1 title = OPLS Lysozyme NPT equilibration
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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2 define = -DPOSRES ; position restrain the protein
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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3 ; Run parameters
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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4 integrator = md ; leap-frog integrator
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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5 nsteps = 500 ; 2 * 50000 = 100 ps
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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6 dt = 0.002 ; 2 fs
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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7 ; Output control
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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8 nstxout = 50 ; save coordinates every 1.0 ps
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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9 nstvout = 50 ; save velocities every 1.0 ps
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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10 nstenergy = 50 ; save energies every 1.0 ps
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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11 nstlog = 50 ; update log file every 1.0 ps
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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12 nstxout-compressed = 50 ; save compressed coordinates every 10.0 ps
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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13 ; Bond parameters
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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14 continuation = yes ; Restarting after NVT
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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15 constraint_algorithm = lincs ; holonomic constraints
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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16 constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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17 lincs_iter = 1 ; accuracy of LINCS
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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18 lincs_order = 4 ; also related to accuracy
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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19 ; Neighborsearching
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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20 cutoff-scheme = Verlet
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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21 ns_type = grid ; search neighboring grid cells
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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22 nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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23 rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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24 rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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25 ; Electrostatics
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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26 coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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27 pme_order = 4 ; cubic interpolation
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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28 fourierspacing = 0.16 ; grid spacing for FFT
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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29 ; Temperature coupling is on
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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30 tcoupl = V-rescale ; modified Berendsen thermostat
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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31 tc-grps = Protein Non-Protein ; two coupling groups - more accurate
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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32 tau_t = 0.1 0.1 ; time constant, in ps
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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33 ref_t = 300 300 ; reference temperature, one for each group, in K
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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34 ; Pressure coupling is on
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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35 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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36 pcoupltype = isotropic ; uniform scaling of box vectors
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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37 tau_p = 2.0 ; time constant, in ps
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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38 ref_p = 1.0 ; reference pressure, in bar
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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39 compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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40 refcoord_scaling = com
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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41 ; Periodic boundary conditions
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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42 pbc = xyz ; 3-D PBC
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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43 ; Dispersion correction
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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44 DispCorr = EnerPres ; account for cut-off vdW scheme
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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45 ; Velocity generation
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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46 gen_vel = no ; Velocity generation is off