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annotate test-data/ions.mdp @ 2:5b01e6df25a0 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
author chemteam
date Thu, 28 Mar 2019 10:13:01 -0400
parents 69ff679edefd
children
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69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
1 ; ions.mdp - used as input into grompp to generate ions.tpr
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
2 ; Parameters describing what to do, when to stop and what to save
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
3 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
4 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
5 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
6 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
7
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
8 ; 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
9 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
10 cutoff-scheme = Verlet
69ff679edefd planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
11 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
12 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:
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13 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
14 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
15 pbc = xyz ; Periodic Boundary Conditions (yes/no)