--- a/test-data/npt.mdp	Fri May 08 11:27:24 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-title		= OPLS Lysozyme NPT 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	        = yes		; Restarting after NVT 
-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
-refcoord_scaling    = com
-; 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