Mercurial > repos > chemteam > gmx_setup
annotate test-data/minim.mdp @ 6:c7bcae9fe040 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
author | chemteam |
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date | Wed, 20 Nov 2019 11:16:14 -0500 |
parents | 644ca8dfdf28 |
children | 4da9ee404eab |
rev | line source |
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0
644ca8dfdf28
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
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1 ; minim.mdp - used as input into grompp to generate em.tpr |
644ca8dfdf28
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) |
644ca8dfdf28
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 |
644ca8dfdf28
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 |
644ca8dfdf28
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 |
644ca8dfdf28
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
|
6 |
644ca8dfdf28
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 |
644ca8dfdf28
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 |
644ca8dfdf28
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff
changeset
|
9 cutoff-scheme = Verlet |
644ca8dfdf28
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) |
644ca8dfdf28
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 |
644ca8dfdf28
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 |
644ca8dfdf28
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 |
644ca8dfdf28
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) |