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.