[gmx-users] unusual trajectory

[Alex]

Your ligand seems to be crossing a periodic boundary, which is normal. 
Try trjconv -pbc whole.


On 7/22/2018 1:35 PM, Atila Petrosian wrote:
> 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