[gmx-users] polymer in octahedron box pbc problem

gromacs query gromacsquery at gmail.com
Thu Oct 1 13:43:30 CEST 2015

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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