[gmx-users] unusual trajectory

[Atila Petrosian]

Dear gromacs users,

After doing NVT md simulation of CNT + LIG + WATER molecules, I encountered
with unusual structure of LIG molecule in some frames in trajectory viewing
using VMD.

https://1drv.ms/u/s!AveJH4Y30cH0sQu08knJYk7TGc7g

My mdp file for this md is as follows:

define          = -DPOSRES_CNT
integrator = md
nsteps = 500000
dt = 0.002
nstxout         = 0
nstvout         = 0
nstxtcout = 1000
nstenergy = 1000
nstlog = 1000
energygrps      = CNT  LIG  SOL
constraints     = all-bonds
Cutoff-scheme   = Verlet
ns_type = grid
nstlist = 10
rlist = 0.9
rcoulomb = 0.9
rvdw = 0.9
coulombtype = PME
pme_order = 4
fourierspacing = 0.16
tcoupl = V-rescale
tc-grps = CNT_LIG  SOL
tau_t = 0.1  0.1
ref_t = 300  300
pcoupl = no
pbc = xyz
periodic_molecules = yes
gen_vel = no
continuation    = yes


How resolve it?

Best, Atila