[gmx-users] Fwd: Broken chain / fragmentation

[Tasneem Kausar]

Try -pbc whole

On 27 May 2017 18:09, "Biplab Ghosh" <ghosh.biplab at gmail.com> wrote:

> Dear Gromacs users,
>
> My Gromacs simulation on a protein terminated without any error and major
> warning. However, when I see the conformations, I found them broken.
>
> For trajectory conversion, I have used the following commands:
>
> gmx trjconv -s protein-md.tpr -f protein-md.xtc -center -pbc nojump -ur
> compact  -o protein-md-center.xtc
>
> gmx trjconv -s protein-md.tpr -f protein-md-center.xtc -fit rot+trans -o
> protein-md-center-fit.xtc
>
>
>
> I would appreciate any help in figuring out where I am going wrong.
>
> Thank you all
> Biplab.
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