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annotate test-data/minim.mdp @ 4:124c21408519 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 22:26:15 +0000
parents a81256d23782
children
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a81256d23782 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"
chemteam
parents:
diff changeset
1 ; minim.mdp - used as input into grompp to generate em.tpr
a81256d23782 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"
chemteam
parents:
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2 integrator = steep ; Algorithm (steep = steepest descent minimization)
a81256d23782 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"
chemteam
parents:
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3 emtol = 1000.0 ; Stop minimization when the maximum force is less than this value
a81256d23782 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"
chemteam
parents:
diff changeset
4 emstep = 0.01 ; Energy step size
a81256d23782 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"
chemteam
parents:
diff changeset
5 nsteps = 50000 ; Maximum number of (minimization) steps to perform
a81256d23782 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"
chemteam
parents:
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6 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
a81256d23782 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"
chemteam
parents:
diff changeset
7 nstlist = 1 ; Frequency to update the neighbor list and long range forces
a81256d23782 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"
chemteam
parents:
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8 cutoff-scheme = Verlet
a81256d23782 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"
chemteam
parents:
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9 ns_type = grid ; Method to determine neighbor list (simple, grid)
a81256d23782 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"
chemteam
parents:
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10 coulombtype = PME ; Treatment of long range electrostatic interactions
a81256d23782 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"
chemteam
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11 rcoulomb = 1.0 ; Short-range electrostatic cut-off
a81256d23782 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"
chemteam
parents:
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12 rlist = 1.0 ; Cut-off distance for the short-range neighbor list.
a81256d23782 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"
chemteam
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13 rvdw = 1.0 ; Short-range Van der Waals cut-off
a81256d23782 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"
chemteam
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14 pbc = xyz ; Periodic Boundary Conditions (yes/no)
a81256d23782 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"
chemteam
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15 gen-seed = 1