[gmx-users] problem regarding gmx trjconv

[Saumyak Mukherjee]

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?

Thanks and Regards,
Saumyak

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