[gmx-users] NPT equilibration

[Deep Bhattacharya]

Hello,

I am have done NVT and NPT equilibration on my complex which is
protein-carbohydrate solvent complex. I am getting -117.4 bar as my
pressure after NPT.
What could be a possible explanation to this?
I have attached the NPT.mdp below

title = PP
define       =  -DPOSRES -DPOSRES_LIGAND; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 2500000 ; 0.001 * 2500000 = 2500 ps
dt    = 0.001 ; 1 fs
; Output control
nstxout = 0 ; save coordinates every 1.0 ps
nstvout = 0 ; save velocities every 1.0 ps
nstenergy = 0 ; save energies every 1.0 ps
nstlog = 1
nstxtcout   = 0
energygrps  = Protein LIG
; 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         = 1        ;
rcoulomb        = 0.8
rvdw            = 0.8
coulombtype     = Cut-off       ; Particle Mesh Ewald for long-
vdwtype        = cut-off
rlistlong      = 1.4
epsilon-rf     = 61
rlist          = 0.75
; Temperature coupling is on
tcoupl = nose-hoover            ; modified Berendsen thermostat
tc-grps       =Protein_LIG Water_and_ions   ; two coupling groups - more
accurate
tau_t = 2.0  2.0        ; 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        = 6.0            ; 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

Please help.
-- 

*Deep S Bhattacharya*

*Graduate Research Assistant*

Mohs Biomedical Imaging & Nanotechnology Group

Pharmaceutical Sciences

*University of Nebraska Medical Center*

4018 Eppley Science Hall  |  Omaha, NE 68198-6805

office 402.559.4349  | cell 402.906.1640

deep.bhattacharya at unmc.edu.deep.bhattacharya199@gmail.com