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annotate test-data/minim.mdp @ 22:070e3ecc3fda draft default tip

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
author chemteam
date Mon, 24 Oct 2022 22:31:49 +0000
parents 1d4dd4f908d4
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644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
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diff changeset
1 ; minim.mdp - used as input into grompp to generate em.tpr
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4da9ee404eab "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
parents: 0
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2 integrator = steep ; Algorithm (steep = steepest descent minimization)
4da9ee404eab "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
chemteam
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3 emtol = 1000.0 ; Stop minimization when the maximum force is less than this value
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644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
4 emstep = 0.01 ; Energy step size
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4da9ee404eab "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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644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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4da9ee404eab "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
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644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
8 cutoff-scheme = Verlet
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4da9ee404eab "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)
4da9ee404eab "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
4da9ee404eab "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
4da9ee404eab "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.
4da9ee404eab "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
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1d4dd4f908d4 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"
chemteam
parents: 12
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14 pbc = xyz ; Periodic Boundary Conditions (yes/no)
1d4dd4f908d4 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"
chemteam
parents: 12
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15 gen-seed = 1