[gmx-users] polymer in octahedron box pbc problem

[gromacs query]

Hi Victor,

With 'pbc whole' polymer remains broken in pbc and the octahedron box looks
weird too.

JIom

On Thu, Oct 1, 2015 at 2:52 PM, Victor Rosas Garcia <rosas.victor at gmail.com>
wrote:

> Have you tried the option "-pbc whole" instead of "-pbc mol"?
>
> Victor
>
> 2015-10-01 6:43 GMT-05:00 gromacs query <gromacsquery at gmail.com>:
>
> > Hi All,
> >
> > I have linear polymer in octahedron box and when I try to visualise a
> > polymer in octahedraon box then water octahedron box looks as expected
> but
> > my polymer looks broken.
> >
> > trjconv_avx -f input.xtc -o out.xtc -pbc mol -ur compact  -s input.tpr -b
> > 100000
> >
> > I have tried to use -center (whole polymer selection) also but still it
> > looks broken.
> >
> > I want to write some pdbs for some analysis and this way my polymer is
> > broken in pbc.
> >
> > Thanks for any suggestions.
> > JIom
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