[gmx-users] unusual trajectory

[Dallas Warren]

Not an unusual structure at all.  That is an issue with how VMD draws
molecules, the bonds between them and a molecule appearing to be
"broken" across the periodic boundary.

VMD guesses where the bonds are, based on distances between the atoms,
and they are formed when it first loads the molecule.  If you then
load a trajectory on top of that, then where ever the atoms are within
the box, VMD will keep drawing the bond between the same atoms.  When
some atoms within the molecule reach the "edge" of the box, and pass
to the other side via the periodic boundary condition, then suddenly
VMD draws a bond right the way across the box, even though the bond
actually is just through the side of the box, via the PBC.  If don't
want to do any processing of the trajectory file, simply use
"DynamicBonds" as the Drawing Method in VMD.  This means VMD will
redraw the bonds in each frame of the trajectory, draw back is it can
be significantly slower when viewing a trajectory.  Best solution, as
already mentioned, is to use the gmx trjconv command with -pbc whole.
That means that in each frame it will save the molecule's coordinates
so that it is all in one piece, and not spanning one of the periodic
boundaries.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Mon, 23 Jul 2018 at 05:35, Atila Petrosian <atila.petrosian at gmail.com> 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
> --
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