[gmx-users] Protein coming out of simulation box.

Mark Abraham mark.j.abraham at gmail.com
Thu Aug 3 11:15:43 CEST 2017


Please check out the GROMACS FAQs. Your protein can't come out of a
periodic cell


On Thu, 3 Aug 2017 10:26 <zaved at tezu.ernet.in> wrote:

> Hello
> I had performed a 100ns protein simulation with gromacs 5.1.4.
> After the simulation I observed that the protein is coming out of the box.
> I have used the following commands to correct it:
> gmx_mpi trjconv -f md.xtc -s md.tpr -pbc mol -ur compact -center -o out.xtc
> gmx_mpi trjconv -f out.xtc -s md.tpr -dt 100 -o file.pdb
> Part of the protein is still out of the box (in the file.pdb).
> Please suggest.
> Thank You
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