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

[Mark Abraham]

Hi,

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

Mark

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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