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annotate test-data/minim.mdp @ 11:8b2553f4f114 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3846f6c5a15ba0586afbd5c901229e237a4e4f17"
author chemteam
date Fri, 08 May 2020 07:48:05 -0400
parents 644ca8dfdf28
children 4da9ee404eab
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644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
1 ; minim.mdp - used as input into grompp to generate em.tpr
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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2 integrator = steep ; Algorithm (steep = steepest descent minimization)
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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3 emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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4 emstep = 0.01 ; Energy step size
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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5 nsteps = 50000 ; Maximum number of (minimization) steps to perform
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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6
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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7 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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8 nstlist = 1 ; Frequency to update the neighbor list and long range forces
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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9 cutoff-scheme = Verlet
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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10 ns_type = grid ; Method to determine neighbor list (simple, grid)
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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11 coulombtype = PME ; Treatment of long range electrostatic interactions
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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12 rcoulomb = 1.0 ; Short-range electrostatic cut-off
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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13 rvdw = 1.0 ; Short-range Van der Waals cut-off
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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14 pbc = xyz ; Periodic Boundary Conditions (yes/no)