[gmx-users] unusual trajectory
Atila Petrosian
atila.petrosian at gmail.com
Sun Jul 22 21:35:51 CEST 2018
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
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