From: "Zhou Bo" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: <[email protected]>
Subject: [gmx-users] AFM Pulling and com motion
Date: Thu, 20 Sep 2007 11:06:09 +0800
Hi GXM Users,
I'm trying to execute some AFM Pulling. I followed the pull code
tutorial
from GMX WORKSHOP 2007, and I found there is no specific to com motion in
mdp, so the default is "comm-mode=Linear" and "comm-grps=System". I was
confused about it as I believed we should not stopcm when doing AFM Pulling
because of the external force. Does it problematic to stopcm when doing AFM
Pulling?
Thanks!
This depends on what type of pulling you are doing.
If you have an absolute reference you are right.
But when you pull between two groups of atoms, there are no
external forces, but internal forces between two groups.
Berk.
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