--- a/test-data/md.mdp	Fri May 08 07:47:05 2020 -0400
+++ b/test-data/md.mdp	Wed May 20 13:02:17 2020 -0400
@@ -1,46 +1,50 @@
-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 
+
+                    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    ; group(s) to write to the compressed trajectory file
+                    ; 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 cut-off
+                    rlist       = 1.0 ; Cut-off distance for the short-range neighbor list.
+                    rvdw        = 1.0    ; Short-range Van der Waals cut-off
+                    ; Electrostatics
+                    coulombtype      = PME    ; method for electrostatics calculations e.g. PME
+                    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
+                    ; 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
+                    ; 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
+
+            
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