[gmx-users] how to visualize gromacs trajectory

[Justin Lemkul]

On 7/3/19 5:27 AM, sunyeping wrote:
> Hi, Steph
>
> I used the following command to repair the trajectory:
>
> gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_center.xtc -center  -pbc mol -ur compact
>
> the bond stretching has disappeared, but the subunits of the protein seperate from each other. How to deal with this? Would it be useful to repeat the trjconv command?

http://manual.gromacs.org/current/user-guide/terminology.html#suggested-workflow

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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