Mercurial > repos > chemteam > gmx_sim
annotate test-data/minim.mdp @ 9:a97dcfc23b4b draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author | chemteam |
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date | Wed, 20 May 2020 13:00:42 -0400 |
parents | 1a5960636405 |
children | da8753545526 |
rev | line source |
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1a5960636405
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents:
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1 ; minim.mdp - used as input into grompp to generate em.tpr |
9
a97dcfc23b4b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents:
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2 integrator = steep ; Algorithm (steep = steepest descent minimization) |
a97dcfc23b4b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents:
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changeset
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3 emtol = 1000.0 ; Stop minimization when the maximum force is less than this value |
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1a5960636405
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents:
diff
changeset
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4 emstep = 0.01 ; Energy step size |
9
a97dcfc23b4b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents:
0
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changeset
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5 nsteps = 50000 ; Maximum number of (minimization) steps to perform |
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1a5960636405
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents:
diff
changeset
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6 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions |
9
a97dcfc23b4b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents:
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changeset
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7 nstlist = 1 ; Frequency to update the neighbor list and long range forces |
0
1a5960636405
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents:
diff
changeset
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8 cutoff-scheme = Verlet |
9
a97dcfc23b4b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents:
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changeset
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9 ns_type = grid ; Method to determine neighbor list (simple, grid) |
a97dcfc23b4b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents:
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changeset
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10 coulombtype = PME ; Treatment of long range electrostatic interactions |
a97dcfc23b4b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents:
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11 rcoulomb = 1.0 ; Short-range electrostatic cut-off |
a97dcfc23b4b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents:
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12 rlist = 1.0 ; Cut-off distance for the short-range neighbor list. |
a97dcfc23b4b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents:
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changeset
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13 rvdw = 1.0 ; Short-range Van der Waals cut-off |
a97dcfc23b4b
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents:
0
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14 pbc = xyz ; Periodic Boundary Conditions (yes/no) |