[gmx-users] AFM Pulling and com motion

[Berk Hess]

>From: "Zhou Bo" <homeboyzb at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: <gmx-users at gromacs.org>
>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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