[gmx-users] polymer in octahedron box pbc problem
Victor Rosas Garcia
rosas.victor at gmail.com
Thu Oct 1 15:52:25 CEST 2015
Have you tried the option "-pbc whole" instead of "-pbc mol"?
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
> 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.
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