[gmx-users] PBC issue

Christopher Neale chris.neale at alum.utoronto.ca
Sat Jul 4 09:39:33 CEST 2015

If you just want to make a new, larger water box, try editconf to make the box larger and then genbox to add water. Any help beyond than that requires us to guess at at least four questions:

What is an "unloading simulation"
How did you "pull a protein"
What exactly do you mean by "both ends of the protein run out of the boundary after pulling"
Where should your protein ends connect?

You'll likely get more help if you can be more specific about what you did and what the problem is.


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of tm651209 <tm651209 at 163.com>
Sent: 03 July 2015 06:29
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] PBC issue

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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