Mercurial > repos > chemteam > gmx_rmsf

annotate test-data/minim.mdp @ 0:f261fded9631 draft default tip

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/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
author chemteam
date Mon, 24 Oct 2022 22:35:01 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
chemteam
parents:
diff changeset
1 ; minim.mdp - used as input into grompp to generate em.tpr
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
chemteam
parents:
diff changeset
2 integrator = steep ; Algorithm (steep = steepest descent minimization)
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
chemteam
parents:
diff changeset
3 emtol = 1000.0 ; Stop minimization when the maximum force is less than this value
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
chemteam
parents:
diff changeset
4 emstep = 0.01 ; Energy step size
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
chemteam
parents:
diff changeset
5 nsteps = 50000 ; Maximum number of (minimization) steps to perform
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
chemteam
parents:
diff changeset
6 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
chemteam
parents:
diff changeset
7 nstlist = 1 ; Frequency to update the neighbor list and long range forces
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
chemteam
parents:
diff changeset
8 cutoff-scheme = Verlet
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
chemteam
parents:
diff changeset
9 ns_type = grid ; Method to determine neighbor list (simple, grid)
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
chemteam
parents:
diff changeset
10 coulombtype = PME ; Treatment of long range electrostatic interactions
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
chemteam
parents:
diff changeset
11 rcoulomb = 1.0 ; Short-range electrostatic cut-off
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
chemteam
parents:
diff changeset
12 rlist = 1.0 ; Cut-off distance for the short-range neighbor list.
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
chemteam
parents:
diff changeset
13 rvdw = 1.0 ; Short-range Van der Waals cut-off
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
chemteam
parents:
diff changeset
14 pbc = xyz ; Periodic Boundary Conditions (yes/no)
f261fded9631 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
chemteam
parents:
diff changeset
15 gen-seed = 1