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view test-data/minim.mdp @ 10:f197e34c33a9 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
author chemteam
date Tue, 20 Oct 2020 10:39:26 +0000
parents a97dcfc23b4b
children da8753545526
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; minim.mdp - used as input into grompp to generate em.tpr
integrator  = steep    ; Algorithm (steep = steepest descent minimization)
emtol    = 1000.0     ; Stop minimization when the maximum force is less than this value
emstep      = 0.01      ; Energy step size
nsteps    = 50000      ; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist        = 1        ; Frequency to update the neighbor list and long range forces
cutoff-scheme   = Verlet
ns_type        = grid    ; Method to determine neighbor list (simple, grid)
coulombtype      = PME    ; Treatment of long range electrostatic interactions
rcoulomb      = 1.0    ; Short-range electrostatic cut-off
rlist       = 1.0 ; Cut-off distance for the short-range neighbor list.
rvdw        = 1.0    ; Short-range Van der Waals cut-off
pbc            = xyz     ; Periodic Boundary Conditions (yes/no)