Mercurial > repos > chemteam > gmx_energy
annotate test-data/minim.mdp @ 14:593c63b5aff8 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 5536c9fbb2f680a5f296db81362099e5a68e0587"
author | chemteam |
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date | Tue, 22 Mar 2022 17:42:04 +0000 |
parents | 6dbf73a62977 |
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5b0e6c2039a7
"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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c8d2c0162b6e
"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) |
c8d2c0162b6e
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents:
0
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3 emtol = 1000.0 ; Stop minimization when the maximum force is less than this value |
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5b0e6c2039a7
"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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c8d2c0162b6e
"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 |
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5b0e6c2039a7
"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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c8d2c0162b6e
"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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7 nstlist = 1 ; Frequency to update the neighbor list and long range forces |
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5b0e6c2039a7
"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 |
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c8d2c0162b6e
"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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9 ns_type = grid ; Method to determine neighbor list (simple, grid) |
c8d2c0162b6e
"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 |
c8d2c0162b6e
"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 |
c8d2c0162b6e
"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. |
c8d2c0162b6e
"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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6dbf73a62977
"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) |
6dbf73a62977
"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 |