[gmx-users] periodic-molecules = yes and movie

Justin Lemkul jalemkul at vt.edu
Tue Aug 7 14:30:09 CEST 2018

On 8/7/18 8:23 AM, Alex wrote:
> Dear all,
> In the simulation of a system in which there is slab, I did not use
> "periodic-molecules
> = yes" unfortunately, hence I can not make a good movie out of the

This is not some magic setting that will make nice movies. Note that a 
"periodic molecule" is different from just normal PBC. Periodic 
molecules are "infinite" molecules like sheets, nanotubes, etc. that 
have bonds between central image atoms and periodic copies of atoms. If 
you needed such a setting and did not use it, likely your simulation 
would have collapsed.

> trajectory using VMD, the slab move during the movie. The simulation is
> around 300 ns and I do not want to just waste the CPU time, so, I wonder if
> there is still any solution for that to make a good movie out of that
> trajectory?

Many of the normal trjconv routines could likely help here. Accounting 
for PBC effects like these is a standard first step in post-processing 
any trajectory.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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