Mercurial > repos > chemteam > gmx_npt

annotate test-data/minim.mdp @ 0:69ff679edefd 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 177cab098ac548bfdecba9d9f04614aec5f6c618
author chemteam
date Thu, 04 Oct 2018 17:38:27 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
1 ; minim.mdp - used as input into grompp to generate em.tpr
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
2 integrator = steep ; Algorithm (steep = steepest descent minimization)
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
3 emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
4 emstep = 0.01 ; Energy step size
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
5 nsteps = 50000 ; Maximum number of (minimization) steps to perform
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
6
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
7 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
8 nstlist = 1 ; Frequency to update the neighbor list and long range forces
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
9 cutoff-scheme = Verlet
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
10 ns_type = grid ; Method to determine neighbor list (simple, grid)
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
11 coulombtype = PME ; Treatment of long range electrostatic interactions
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
12 rcoulomb = 1.0 ; Short-range electrostatic cut-off
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
13 rvdw = 1.0 ; Short-range Van der Waals cut-off
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
14 pbc = xyz ; Periodic Boundary Conditions (yes/no)