md.mdp.rtf

title                   = OPLS Lysozyme NPT equilibration\
; Run parameters\
integrator              = md        ; leap-frog integrator\
nsteps                  = 50000000    ; 2 * 50000000 = 100 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               = 10000      ; save energies every 10.0 ps\
nstlog                  = 10000      ; update log file every 10.0 ps\
nstxout-compressed      = 10000      ; 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\
; Neighborsearching\
cutoff-scheme           = Verlet    ; Buffered neighbor searching\
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}