NPT

mdp file for NPT run

title  = your system NPT equilibration 
define  = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md  ; leap-frog integrator
nsteps  = 50000  ; 2 * 50000 = 100 ps
dt  = 0.002  ; 2 fs
; Output control
nstxout  = 100  ; save coordinates every 0.2 ps
nstvout  = 100  ; save velocities every 0.2 ps
nstenergy = 100  ; save energies every 0.2 ps
nstlog  = 100  ; update log file every 0.2 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
ns_type  = grid  ; search neighboring grid cells
nstlist  = 5  ; 10 fs
rlist  = 1.0  ; short-range neighborlist cutoff (in nm)
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