[gmx-users] PBC issue

tm651209 tm651209 at 163.com
Fri Jul 3 12:45:12 CEST 2015

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.

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