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view test-data/minim.mdp @ 3:4dba9a5b74fc draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 43df863472247b5da304627b6b863c47ab7d02fa"
author chemteam
date Sun, 01 Dec 2019 09:14:59 -0500
parents 1a5960636405
children a97dcfc23b4b
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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 < 1000.0 kJ/mol/nm
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
rvdw		    = 1.0		; Short-range Van der Waals cut-off
pbc		        = xyz 		; Periodic Boundary Conditions (yes/no)