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comparison test-data/minim.mdp @ 9:a97dcfc23b4b draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author chemteam
date Wed, 20 May 2020 13:00:42 -0400
parents 1a5960636405
children da8753545526
comparison
equal deleted inserted replaced
8:4b4232c98b6e 9:a97dcfc23b4b
1 ; minim.mdp - used as input into grompp to generate em.tpr 1 ; minim.mdp - used as input into grompp to generate em.tpr
2 integrator = steep ; Algorithm (steep = steepest descent minimization) 2 integrator = steep ; Algorithm (steep = steepest descent minimization)
3 emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm 3 emtol = 1000.0 ; Stop minimization when the maximum force is less than this value
4 emstep = 0.01 ; Energy step size 4 emstep = 0.01 ; Energy step size
5 nsteps = 50000 ; Maximum number of (minimization) steps to perform 5 nsteps = 50000 ; Maximum number of (minimization) steps to perform
6
7 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions 6 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
8 nstlist = 1 ; Frequency to update the neighbor list and long range forces 7 nstlist = 1 ; Frequency to update the neighbor list and long range forces
9 cutoff-scheme = Verlet 8 cutoff-scheme = Verlet
10 ns_type = grid ; Method to determine neighbor list (simple, grid) 9 ns_type = grid ; Method to determine neighbor list (simple, grid)
11 coulombtype = PME ; Treatment of long range electrostatic interactions 10 coulombtype = PME ; Treatment of long range electrostatic interactions
12 rcoulomb = 1.0 ; Short-range electrostatic cut-off 11 rcoulomb = 1.0 ; Short-range electrostatic cut-off
13 rvdw = 1.0 ; Short-range Van der Waals cut-off 12 rlist = 1.0 ; Cut-off distance for the short-range neighbor list.
14 pbc = xyz ; Periodic Boundary Conditions (yes/no) 13 rvdw = 1.0 ; Short-range Van der Waals cut-off
14 pbc = xyz ; Periodic Boundary Conditions (yes/no)