Mercurial > repos > chemteam > gmx_solvate
annotate test-data/ions.mdp @ 7:589652e8eb31 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1"
author | chemteam |
---|---|
date | Wed, 18 Dec 2019 15:23:05 -0500 |
parents | 77aaf9a68166 |
children |
rev | line source |
---|---|
0
77aaf9a68166
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
chemteam
parents:
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
parents:
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
parents:
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:
diff
changeset
|
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) |