[gmx-users] problem regarding gmx trjconv

Saumyak Mukherjee mukherjee.saumyak50 at gmail.com
Thu May 2 13:00:32 CEST 2019

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


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?

Thanks and Regards,

*Saumyak Mukherjee*
Senior Research Fellow
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bengaluru - 560012

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