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annotate test-data/ions.mdp @ 0:77aaf9a68166 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
author chemteam
date Thu, 04 Oct 2018 18:22:34 -0400
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77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
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diff changeset
1 ; ions.mdp - used as input into grompp to generate ions.tpr
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
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diff changeset
2 ; Parameters describing what to do, when to stop and what to save
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
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diff changeset
3 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:
diff changeset
4 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
5 emstep = 0.01 ; Energy step size
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
6 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:
diff changeset
7
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
8 ; 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
9 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:
diff changeset
10 cutoff-scheme = Verlet
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
diff changeset
11 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:
diff changeset
12 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
parents:
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13 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:
diff changeset
14 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:
diff changeset
15 pbc = xyz ; Periodic Boundary Conditions (yes/no)