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annotate test-data/minim.mdp @ 10:07d3925e6141 draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author chemteam
date Wed, 20 May 2020 16:53:15 +0000
parents e79733545528
children
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e79733545528 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
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diff changeset
1 ; minim.mdp - used as input into grompp to generate em.tpr
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07d3925e6141 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
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2 integrator = steep ; Algorithm (steep = steepest descent minimization)
07d3925e6141 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
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diff changeset
3 emtol = 1000.0 ; Stop minimization when the maximum force is less than this value
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e79733545528 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
4 emstep = 0.01 ; Energy step size
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07d3925e6141 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 0
diff changeset
5 nsteps = 50000 ; Maximum number of (minimization) steps to perform
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e79733545528 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
6 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
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07d3925e6141 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 0
diff changeset
7 nstlist = 1 ; Frequency to update the neighbor list and long range forces
0
e79733545528 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
chemteam
parents:
diff changeset
8 cutoff-scheme = Verlet
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07d3925e6141 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 0
diff changeset
9 ns_type = grid ; Method to determine neighbor list (simple, grid)
07d3925e6141 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 0
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10 coulombtype = PME ; Treatment of long range electrostatic interactions
07d3925e6141 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 0
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11 rcoulomb = 1.0 ; Short-range electrostatic cut-off
07d3925e6141 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 0
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12 rlist = 1.0 ; Cut-off distance for the short-range neighbor list.
07d3925e6141 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 0
diff changeset
13 rvdw = 1.0 ; Short-range Van der Waals cut-off
07d3925e6141 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 0
diff changeset
14 pbc = xyz ; Periodic Boundary Conditions (yes/no)