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

[Alex]

Thanks.

On Tue, Aug 7, 2018 at 8:30 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.

No, the simulation did not blow up and worked nicely. As far as I
understood and in general the periodic-molecule = yes should be used when a
surface is connected to it's image in the neighbouring cell, mine is silica
slab, and if the the slab is defined only by non-bonded interaction like
most of the metallic slab the periodic molecule = NO should work finely in
spite of being infinite.


> > 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.
> Actually what I see is the result of two below comments applied over the
> initial trajectory:
>

gmx_mpi trjconv -f prd.xtc -s eql1.gro -o nojump-skip-30-prd.xtc -center
-pbc nojump -n input/index.ndx -tu ns -skip 30   < choice : salb, system
gmx_mpi trjconv -f nojump-skip-30-prd.xtc -s prd.tpr -o
nopbc-nojump-skip-30-prd.xtc -center -pbc whole -ur compact -n
input/index.ndx -tu ns < choice : salb, system

Regards,
Alex

> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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> Blacksburg, VA 24061
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