Mercurial > repos > chemteam > gmx_makendx

diff test-data/nvt.mdp @ 6:7b530c213ec7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author chemteam
date Wed, 20 May 2020 16:50:52 +0000
parents acb462ccdcbc
children
line wrap: on
line diff
--- a/test-data/nvt.mdp	Fri May 08 11:24:36 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-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