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annotate test-data/md.mdp @ 0:a5afe283962d draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
author chemteam
date Wed, 01 Dec 2021 15:34:01 +0000
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a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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1
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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2 title = OPLS Lysozyme MD simulation
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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3 ; Run parameters
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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4 integrator = md ; leap-frog integrator
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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5 nsteps = 500 ; 2 * 500000 = 1000 ps (1 ns)
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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6 dt = 0.002 ; 2 fs
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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7 ; Output control
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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8 nstxout = 50 ; save coordinates every 10.0 ps
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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9 nstvout = 50 ; save velocities every 10.0 ps
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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10 nstenergy = 50 ; save energies every 10.0 ps
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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11 nstlog = 50 ; update log file every 10.0 ps
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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12 nstxout-compressed = 50 ; save compressed coordinates every 10.0 ps
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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13 ; nstxout-compressed replaces nstxtcout
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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14 compressed-x-grps = System ; group(s) to write to the compressed trajectory file
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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15 ; Bond parameters
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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16 continuation = yes ; Restarting after NPT
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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17 constraint_algorithm = lincs ; holonomic constraints
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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18 constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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19 lincs_iter = 1 ; accuracy of LINCS
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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20 lincs_order = 4 ; also related to accuracy
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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21 ; Neighborsearching
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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22 cutoff-scheme = Verlet
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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23 ns_type = grid ; search neighboring grid cells
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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24 nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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25 rcoulomb = 1.0 ; Short-range electrostatic cut-off
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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26 rlist = 1.0 ; Cut-off distance for the short-range neighbor list.
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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27 rvdw = 1.0 ; Short-range Van der Waals cut-off
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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28 ; Electrostatics
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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29 coulombtype = PME ; method for electrostatics calculations e.g. PME
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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30 pme_order = 4 ; cubic interpolation
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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31 fourierspacing = 0.16 ; grid spacing for FFT
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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32 ; Temperature coupling is on
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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33 tcoupl = V-rescale ; modified Berendsen thermostat
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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34 tc-grps = Protein Non-Protein ; two coupling groups - more accurate
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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35 tau_t = 0.1 0.1 ; time constant, in ps
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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36 ref_t = 300 300 ; reference temperature, one for each group, in K
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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37 ; Periodic boundary conditions
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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38 pbc = xyz ; 3-D PBC
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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39 ; Dispersion correction
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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40 DispCorr = EnerPres ; account for cut-off vdW scheme
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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41 ; Velocity generation
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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42 gen_vel = no ; Velocity generation is off
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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43 ; Pressure coupling is on
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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44 pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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45 pcoupltype = isotropic ; uniform scaling of box vectors
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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46 tau_p = 2.0 ; time constant, in ps
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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47 ref_p = 1.0 ; reference pressure, in bar
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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48 compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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49
a5afe283962d "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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