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diff test-data/nvt.mdp @ 0:77aaf9a68166 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
author chemteam
date Thu, 04 Oct 2018 18:22:34 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nvt.mdp	Thu Oct 04 18:22:34 2018 -0400
@@ -0,0 +1,43 @@
+title		= OPLS Lysozyme NVT equilibration 
+define		= -DPOSRES	; position restrain the protein
+; Run parameters
+integrator	= md		; leap-frog integrator
+nsteps		= 500		; 2 * 50000 = 100 ps
+dt		    = 0.002		; 2 fs
+; Output control
+nstxout		= 50		; save coordinates every 1.0 ps
+nstvout		= 50		; save velocities every 1.0 ps
+nstenergy	= 50		; save energies every 1.0 ps
+nstlog		= 50		; update log file every 1.0 ps
+nstxout-compressed  = 50      ; save compressed coordinates every 10.0 ps
+; Bond parameters
+continuation	        = no		; first dynamics run
+constraint_algorithm    = lincs	    ; holonomic constraints 
+constraints	            = all-bonds	; all bonds (even heavy atom-H bonds) constrained
+lincs_iter	            = 1		    ; accuracy of LINCS
+lincs_order	            = 4		    ; also related to accuracy
+; Neighborsearching
+cutoff-scheme   = Verlet
+ns_type		    = grid		; search neighboring grid cells
+nstlist		    = 10		; 20 fs, largely irrelevant with Verlet
+rcoulomb	    = 1.0		; short-range electrostatic cutoff (in nm)
+rvdw		    = 1.0		; short-range van der Waals cutoff (in nm)
+; Electrostatics
+coulombtype	    = PME	; Particle Mesh Ewald for long-range electrostatics
+pme_order	    = 4		; cubic interpolation
+fourierspacing	= 0.16	; grid spacing for FFT
+; Temperature coupling is on
+tcoupl		= V-rescale	            ; modified Berendsen thermostat
+tc-grps		= Protein Non-Protein	; two coupling groups - more accurate
+tau_t		= 0.1	  0.1           ; time constant, in ps
+ref_t		= 300 	  300           ; reference temperature, one for each group, in K
+; Pressure coupling is off
+pcoupl		= no 		; no pressure coupling in NVT
+; Periodic boundary conditions
+pbc		= xyz		    ; 3-D PBC
+; Dispersion correction
+DispCorr	= EnerPres	; account for cut-off vdW scheme
+; Velocity generation
+gen_vel		= yes		; assign velocities from Maxwell distribution
+gen_temp	= 300		; temperature for Maxwell distribution
+gen_seed	= -1		; generate a random seed