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diff test-data/ions.mdp @ 0:bb0053c4e4f2 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
author chemteam
date Tue, 21 Jan 2020 07:29:43 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ions.mdp	Tue Jan 21 07:29:43 2020 -0500
@@ -0,0 +1,15 @@
+; ions.mdp - used as input into grompp to generate ions.tpr
+; Parameters describing what to do, when to stop and what to save
+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)