[gmx-users] problem in NPT equilibration

[soumadwip ghosh]

Hello,
        I have been trying to simulate a double stranded DNA in water in
presence of ions having hydrophobic sites. What I am doing after energy
minimization is to elevate the temperature of the system to 300 K in 100 ps
in the NPT ensemble and after that I am equilibriating the system under NPT
conditions for 10 ns. But I am not getting the pressure fixed at 1 bar when
I am checking it. The details of my NPT.mdp file and the outcomes are given
below.

Kindly help me.

Thanks and regards,
Soumadwip

title           = OPLS Lysozyme NPT equilibration
define          = -DPOSRES      ; position restrain the protein
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 5000000               ; 2 * 500000 = 1000 ps
dt              = 0.002         ; 2 fs
; Output control
nstxout         = 0             ; save coordinates every 0.2 ps
nstvout         = 0             ; save velocities every 0.2 ps
nstenergy       = 0             ; save energies every 0.2 ps
nstlog          = 1000          ; 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             ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1             ; short-range electrostatic cutoff (in nm)
rvdw            = 1             ; 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         = DNA   SOL     ION     ; three coupling groups - more
accurate
tau_t           = 0.1   0.1     0.1     ; time constant, in ps
ref_t           = 300   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
~
~

I am getting 37 bar pressure with RMSD, total drift and err estimate all
zero.