Mercurial > repos > chemteam > gmx_setup

annotate test-data/ions.mdp @ 4:b43abebffad6 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:50:01 -0400
parents 644ca8dfdf28
children
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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 ; ions.mdp - used as input into grompp to generate ions.tpr
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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2 ; Parameters describing what to do, when to stop and what to save
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
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3 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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4 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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5 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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6 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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7
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
chemteam
parents:
diff changeset
8 ; 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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9 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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10 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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11 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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12 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
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13 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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14 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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15 pbc = xyz ; Periodic Boundary Conditions (yes/no)