[gmx-users] problem regarding gmx trjconv

Justin Lemkul jalemkul at vt.edu
Thu May 2 18:56:24 CEST 2019

On 5/2/19 6:59 AM, Saumyak Mukherjee wrote:
> Dear All,
> I have an insulin hexamer, which (because of PBC)  apparently breaks into
> pieces after simulation.
> To make the molecule whole, I use the following command:
> gmx trjconv -f traj.xtc -s md.tpr -o traj_whole.xtc -pbc cluster
> or
> gmx trjconv -f traj.xtc -s md.tpr -o traj_whole.xtc -pbc mol -ur compact
> This command(s) makes each chain (out of the 6) whole, but the chains do
> not come together. So the hexamer as a whole still remains broken.
> Is there a way to solve this problem?

Use -center with an index group corresponding to residues that 
constitute the interface of one protein.



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