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annotate test-data/minim.mdp @ 3:7161b230adad draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:47:31 -0400
parents 77aaf9a68166
children 27ea4e1a3f95
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77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
1 ; minim.mdp - used as input into grompp to generate em.tpr
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
2 integrator = steep ; Algorithm (steep = steepest descent minimization)
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
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3 emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
4 emstep = 0.01 ; Energy step size
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
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5 nsteps = 50000 ; Maximum number of (minimization) steps to perform
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
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6
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
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7 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
8 nstlist = 1 ; Frequency to update the neighbor list and long range forces
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
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9 cutoff-scheme = Verlet
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
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10 ns_type = grid ; Method to determine neighbor list (simple, grid)
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
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11 coulombtype = PME ; Treatment of long range electrostatic interactions
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
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12 rcoulomb = 1.0 ; Short-range electrostatic cut-off
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
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13 rvdw = 1.0 ; Short-range Van der Waals cut-off
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
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14 pbc = xyz ; Periodic Boundary Conditions (yes/no)