title                   = OPLS Lysozyme MD run 
; Run parameters
integrator              = md        ; leap-frog integrator
nsteps                  = 5000000   ; 2 * 2500000 = 10000 ps (10 ns)
dt                      = 0.002     ; 2 fs
; Output control
nstxout                 = 0         ; suppress bulky .trr file by specifying 
nstvout                 = 0         ; 0 for output frequency of nstxout,
nstfout                 = 0         ; nstvout, and nstfout
nstenergy               = 5000      ; save energies every 10.0 ps
nstlog                  = 5000      ; update log file every 10.0 ps
nstxout-compressed      = 5000      ; save compressed coordinates every 10.0 ps
compressed-x-grps       = System    ; save the whole system
; Bond parameters
continuation            = yes       ; Restarting after NPT 
constraint_algorithm    = lincs     ; holonomic constraints 
constraints             = h-bonds   ; bonds involving H are constrained
lincs_iter              = 1         ; accuracy of LINCS
lincs_order             = 4         ; also related to accuracy
; Nonbonded settings 
cutoff-scheme           = Verlet    ; Buffered neighbor searching
ns_type                 = grid      ; search neighboring grid cells
nstlist                 = 10        ; 20 fs, largely irrelevant with Verlet scheme
; vdW
rvdw                    = 1.2       ; short-range van der Waals cutoff (in nm)
rvdw-switch             = 1.0
vdw-modifier            = force-switch
DispCorr                = No
; Electrostatics
rcoulomb                = 1.2       ; short-range electrostatic cutoff (in nm)
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                 = System 
tau_t                   = 1.0
ref_t                   = 298 
; Pressure coupling is on
pcoupl                  = C-rescale 
pcoupltype              = isotropic             ; uniform scaling of box vectors
tau_p                   = 5.0                   ; 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
; Velocity generation
gen_vel                 = no        ; Velocity generation is off