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annotate test-data/minim.mdp @ 0:7f64dd60f5d7 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
author chemteam
date Mon, 24 Oct 2022 22:12:01 +0000
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7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
chemteam
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1 ; minim.mdp - used as input into grompp to generate em.tpr
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
chemteam
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diff changeset
2 integrator = steep ; Algorithm (steep = steepest descent minimization)
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
chemteam
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diff changeset
3 emtol = 1000.0 ; Stop minimization when the maximum force is less than this value
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
chemteam
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diff changeset
4 emstep = 0.01 ; Energy step size
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
chemteam
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5 nsteps = 50000 ; Maximum number of (minimization) steps to perform
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
chemteam
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diff changeset
6 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
chemteam
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diff changeset
7 nstlist = 1 ; Frequency to update the neighbor list and long range forces
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
chemteam
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8 cutoff-scheme = Verlet
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
chemteam
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9 ns_type = grid ; Method to determine neighbor list (simple, grid)
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
chemteam
parents:
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10 coulombtype = PME ; Treatment of long range electrostatic interactions
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
chemteam
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11 rcoulomb = 1.0 ; Short-range electrostatic cut-off
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
chemteam
parents:
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12 rlist = 1.0 ; Cut-off distance for the short-range neighbor list.
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
chemteam
parents:
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13 rvdw = 1.0 ; Short-range Van der Waals cut-off
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
chemteam
parents:
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14 pbc = xyz ; Periodic Boundary Conditions (yes/no)
7f64dd60f5d7 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 27f3e0b555b8178299ada42df33006e2f69b4e80
chemteam
parents:
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15 gen-seed = 1