[gmx-users] CNT md simulation & unusual Equilibrated structure (NVT)

[Atila Petrosian]

Hi all,

Excuse me for my questions.

After energy minimization, I did NVT equilibration phase. Unfortunately, I
did not find an appropriate tutorial and mdp file for CNT simulation. I
used  following mdp file:

integrator = md
nsteps = 50000
dt     = 0.002
energygrps = CNT LIG
nstxout = 500
nstvout = 500
nstenergy = 500
nstlog = 500
periodic_molecules       = yes
continuation = no
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 1
lincs_order = 4
ns_type = grid
nstlist = 20
rlist = 0.9
rcoulomb = 0.9
vdwtype     = Cut-off
rvdw = 0.9
Cutoff-scheme   = Verlet
coulombtype = PME
pme_order = 4
ewald_rtol               = 1e-5
fourierspacing = 4
tcoupl = V-rescale
tc-grps = CNT_LIG  SOL
tau_t = 0.1 0.1
ref_t = 300 300
pcoupl = no
pbc = xyz
DispCorr = EnerPres
gen_vel = yes
gen_temp = 300
gen_seed = -1
--------------------------------------------

After NVT equilibration:

https://1drv.ms/u/s!AveJH4Y30cH0sQqBSd6Cmi_sFGCz

Is there wrong parameter in my mdp file?

Best,
Atila