GROMACS version:2020.6
GROMACS modification: No
When I do MD simulation about DES extraction citral, the volume of the box becomes huge after a period of time.And before MD simulation, NVT and NPT has been finished normally, so anyone can tell how to solve this problem?
here is my md.mdp：
define =
integrator = md
dt = 0.001 ; ps
nsteps = 100000000 ; 200ns
comm-grps = system
energygrps =
;
nstxout = 2000
nstvout = 2000
nstfout = 2000
nstlog = 2000
nstenergy = 2000
nstxout-compressed = 2000
compressed-x-grps = system
;
pbc = xyz
cutoff-scheme = Verlet
coulombtype = PME
rcoulomb = 1.2
vdwtype = cut-off
rvdw = 1.2
DispCorr = EnerPres
;
Tcoupl = V-rescale
tau_t = 0.2
tc_grps = system
ref_t = 338.15
;
Pcoupl = parrinello-rahman
pcoupltype = isotropic
tau_p = 2.0
ref_p = 1.0
compressibility = 4.5e-5
;
gen_vel = no
gen_temp = 298.15
gen_seed = -1
;
The period of your PR barostat is 2 ps, which is very short. Likely this couples to a vibrational mode in your system. Increase tau_p or user a newer version of Gromacs and the c-rescale barostat.