[gmx-users] polymer in octahedron box pbc problem

[Victor Rosas Garcia]

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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