Dear all,

I am new to gromacs. For a test I am running a water box NPT calculation using tip4p force field with 370 water molecules in a 2.2 * 2.2 * 2.2 box.

My top file is:

#include “oplsaa.ff/forcefield.itp”

#include “oplsaa.ff/tip4p.itp”

[ System ]

TIP4P in water

[ Molecules ]

SOL 370

and my npt.mdp file is:

title = NPT Equilibration after nvt

; Run parameters

integrator = md ; leap-frog integrator

nsteps = 1500000 ; 2 * 1500000 = 1000 ps (3 ns)

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 = no ; Restarting after NVT

; Neighborsearching

ns_type = grid ; search neighboring grid cels

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

tcouple=Berendsen

ref_t =300

tau_t =0.1 ;time constant in ps

; Pressure coupling is on

pcouple=Berendsen

tau_p =0.1

pcoupletype=isotropic

ref_p =1 ; in bar

; Periodic boundary conditions

pbc = xyz ; 3-D PBC

; Dispersion correction

DispCorr = EnerPres ; account for cut-off vdW scheme

; Velocity generation

gen_vel = yes ; Velocity generation is off

gen_temp = 300 ; temperature for Maxwell distribution

gen_seed = -1 ; generate a random seed

I have run the minimization before NPT calculation. The potential energy converges normally. But with the above settings for the NPT calculation, my total energy goes up as the simulation goes (in total 3 ns).

What is wrong with my input file?

Many thanks for your help.

Best wishes.