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

[Alex]

Thanks.

On Wed, Aug 8, 2018 at 10:16 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/7/18 8:51 AM, Alex wrote:
> > 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.
>
> Correct. "Periodic molecules" only matter for bonded interactions.
>
> >
> >>> 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
>
> If the surface appears to be shifting laterally, then a translational
> fit is probably what you want.

Do you know please any command for that by heart? Or if gromacs has one for
that?

> The surface first shift laterally in the very early steps of the
trajectory, there are also some Up-Down movement in some frames.

Thank you.
Regards,
Alex

>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
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