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

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/md.mdp	Tue Jan 21 07:29:43 2020 -0500
@@ -0,0 +1,46 @@
+title		= OPLS Lysozyme MD simulation 
+; Run parameters
+integrator	= md		; leap-frog integrator
+nsteps		= 500	; 2 * 500000 = 1000 ps (1 ns)
+dt		    = 0.002		; 2 fs
+; Output control
+nstxout		        = 50		; save coordinates every 10.0 ps
+nstvout		        = 50		; save velocities every 10.0 ps
+nstenergy	        = 50		; save energies every 10.0 ps
+nstlog		        = 50		; update log file every 10.0 ps
+nstxout-compressed  = 50      ; save compressed coordinates every 10.0 ps
+                                ; nstxout-compressed replaces nstxtcout
+compressed-x-grps   = System    ; replaces xtc-grps
+; Bond parameters
+continuation	        = yes		; Restarting after NPT 
+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 scheme
+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 on
+pcoupl		        = Parrinello-Rahman	    ; Pressure coupling on in NPT
+pcoupltype	        = isotropic	            ; uniform scaling of box vectors
+tau_p		        = 2.0		            ; time constant, in ps
+ref_p		        = 1.0		            ; reference pressure, in bar
+compressibility     = 4.5e-5	            ; isothermal compressibility of water, bar^-1
+; Periodic boundary conditions
+pbc		= xyz		; 3-D PBC
+; Dispersion correction
+DispCorr	= EnerPres	; account for cut-off vdW scheme
+; Velocity generation
+gen_vel		= no		; Velocity generation is off