Mercurial > repos > chemteam > gmx_restraints
annotate test-data/minim.mdp @ 16:509aa136d4e3 draft default tip
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
author | chemteam |
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date | Mon, 24 Oct 2022 22:27:33 +0000 |
parents | 14a7bf3e03df |
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rev | line source |
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72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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1 ; minim.mdp - used as input into grompp to generate em.tpr |
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ca6a4740114e
"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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2 integrator = steep ; Algorithm (steep = steepest descent minimization) |
ca6a4740114e
"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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3 emtol = 1000.0 ; Stop minimization when the maximum force is less than this value |
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72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
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4 emstep = 0.01 ; Energy step size |
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ca6a4740114e
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents:
0
diff
changeset
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5 nsteps = 50000 ; Maximum number of (minimization) steps to perform |
0
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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 |
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ca6a4740114e
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents:
0
diff
changeset
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7 nstlist = 1 ; Frequency to update the neighbor list and long range forces |
0
72c2b7992c26
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
diff
changeset
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8 cutoff-scheme = Verlet |
6
ca6a4740114e
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents:
0
diff
changeset
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9 ns_type = grid ; Method to determine neighbor list (simple, grid) |
ca6a4740114e
"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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10 coulombtype = PME ; Treatment of long range electrostatic interactions |
ca6a4740114e
"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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11 rcoulomb = 1.0 ; Short-range electrostatic cut-off |
ca6a4740114e
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents:
0
diff
changeset
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12 rlist = 1.0 ; Cut-off distance for the short-range neighbor list. |
ca6a4740114e
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents:
0
diff
changeset
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13 rvdw = 1.0 ; Short-range Van der Waals cut-off |
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14a7bf3e03df
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"
chemteam
parents:
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14 pbc = xyz ; Periodic Boundary Conditions (yes/no) |
14a7bf3e03df
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"
chemteam
parents:
6
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15 gen-seed = 1 |