[gmx-users] problem regarding gmx trjconv
mukherjee.saumyak50 at gmail.com
Thu May 2 13:00:32 CEST 2019
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,
Senior Research Fellow
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bengaluru - 560012
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