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annotate test-data/minim.mdp @ 13:d06c503b33bd draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 7120a24dbb365d0a06595018a3b6f27dad0961e0"
author chemteam
date Mon, 14 Mar 2022 10:35:32 +0000
parents 861b2487aaea
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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 ; minim.mdp - used as input into grompp to generate em.tpr
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bfb65cb551d8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
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2 integrator = steep ; Algorithm (steep = steepest descent minimization)
bfb65cb551d8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
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3 emtol = 1000.0 ; Stop minimization when the maximum force is less than this value
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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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4 emstep = 0.01 ; Energy step size
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bfb65cb551d8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 0
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5 nsteps = 50000 ; Maximum number of (minimization) steps to perform
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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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6 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
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bfb65cb551d8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
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7 nstlist = 1 ; Frequency to update the neighbor list and long range forces
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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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8 cutoff-scheme = Verlet
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bfb65cb551d8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 0
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9 ns_type = grid ; Method to determine neighbor list (simple, grid)
bfb65cb551d8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
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10 coulombtype = PME ; Treatment of long range electrostatic interactions
bfb65cb551d8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 0
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11 rcoulomb = 1.0 ; Short-range electrostatic cut-off
bfb65cb551d8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 0
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12 rlist = 1.0 ; Cut-off distance for the short-range neighbor list.
bfb65cb551d8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 0
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13 rvdw = 1.0 ; Short-range Van der Waals cut-off
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861b2487aaea "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"
chemteam
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14 pbc = xyz ; Periodic Boundary Conditions (yes/no)
861b2487aaea "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"
chemteam
parents: 6
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15 gen-seed = 1