Mercurial > repos > chemteam > gmx_merge_topology_files

annotate test-data/ions.mdp @ 2:f2faba46d680 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:49:26 -0400
parents 33ed3c26b8c2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
1 ; ions.mdp - used as input into grompp to generate ions.tpr
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
2 ; Parameters describing what to do, when to stop and what to save
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
3 integrator = steep ; Algorithm (steep = steepest descent minimization)
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
4 emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
5 emstep = 0.01 ; Energy step size
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
6 nsteps = 50000 ; Maximum number of (minimization) steps to perform
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
7
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
8 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
9 nstlist = 1 ; Frequency to update the neighbor list and long range forces
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
10 cutoff-scheme = Verlet
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
11 ns_type = grid ; Method to determine neighbor list (simple, grid)
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
12 coulombtype = PME ; Treatment of long range electrostatic interactions
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
13 rcoulomb = 1.0 ; Short-range electrostatic cut-off
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
14 rvdw = 1.0 ; Short-range Van der Waals cut-off
33ed3c26b8c2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
15 pbc = xyz ; Periodic Boundary Conditions (yes/no)