[gmx-users] PBC issue

[tm651209]

Dear all,


I pulled a protein using pdc=xyz, and want to do unloading simulation. The problem is both ends of the protein run out of the boundary after pulling. After unloading for a while, I found that both ends did not connect to where they should connect. 
Is there a way that I can regenerate the water box, so that the whole protein can stay inside. Therefore, I can use it as a initial state for unloading simulation.


Thanks very much.
Regards.