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annotate test-data/ions.mdp @ 3:01a435922dd5 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
author chemteam
date Tue, 21 Jan 2020 07:28:50 -0500
parents 48dcca6f45ce
children
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48dcca6f45ce "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff changeset
1 ; ions.mdp - used as input into grompp to generate ions.tpr
48dcca6f45ce "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff changeset
2 ; Parameters describing what to do, when to stop and what to save
48dcca6f45ce "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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3 integrator = steep ; Algorithm (steep = steepest descent minimization)
48dcca6f45ce "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff changeset
4 emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
48dcca6f45ce "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff changeset
5 emstep = 0.01 ; Energy step size
48dcca6f45ce "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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6 nsteps = 50000 ; Maximum number of (minimization) steps to perform
48dcca6f45ce "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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7
48dcca6f45ce "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff changeset
8 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
48dcca6f45ce "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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9 nstlist = 1 ; Frequency to update the neighbor list and long range forces
48dcca6f45ce "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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10 cutoff-scheme = Verlet
48dcca6f45ce "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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11 ns_type = grid ; Method to determine neighbor list (simple, grid)
48dcca6f45ce "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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12 coulombtype = PME ; Treatment of long range electrostatic interactions
48dcca6f45ce "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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13 rcoulomb = 1.0 ; Short-range electrostatic cut-off
48dcca6f45ce "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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14 rvdw = 1.0 ; Short-range Van der Waals cut-off
48dcca6f45ce "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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15 pbc = xyz ; Periodic Boundary Conditions (yes/no)