comparison test-data/ions.mdp @ 0:33ed3c26b8c2 draft

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
author chemteam
date Thu, 28 Mar 2019 10:12:00 -0400
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comparison
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-1:000000000000 0:33ed3c26b8c2
1 ; ions.mdp - used as input into grompp to generate ions.tpr
2 ; Parameters describing what to do, when to stop and what to save
3 integrator = steep ; Algorithm (steep = steepest descent minimization)
4 emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
5 emstep = 0.01 ; Energy step size
6 nsteps = 50000 ; Maximum number of (minimization) steps to perform
7
8 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
9 nstlist = 1 ; Frequency to update the neighbor list and long range forces
10 cutoff-scheme = Verlet
11 ns_type = grid ; Method to determine neighbor list (simple, grid)
12 coulombtype = PME ; Treatment of long range electrostatic interactions
13 rcoulomb = 1.0 ; Short-range electrostatic cut-off
14 rvdw = 1.0 ; Short-range Van der Waals cut-off
15 pbc = xyz ; Periodic Boundary Conditions (yes/no)