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diff test-data/minim.mdp @ 0:644ca8dfdf28 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
author chemteam
date Thu, 04 Oct 2018 17:39:10 -0400
parents
children 4da9ee404eab
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/minim.mdp	Thu Oct 04 17:39:10 2018 -0400
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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)