Ok, that's what we thought. So would you think that it is a better
idea to fix an atom close to the center of mass instead of the center
of mass itself? That way, one shouldn't get any additional forces
acting on the rear end, just forces acting on a single atom in the
center. Would you agree with that?
Thanks,
Kay.
On Jul 18, 2006, at 2:16 PM, Berk Hess wrote:
From: Kay Gottschalk <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: Re: [gmx-users] center of mass pulling in AFM
Date: Tue, 18 Jul 2006 12:44:20 +0200
We have a complex with two chains. From one chain (chain A), we
are fixing the COM. We are pulling on the COM of the other chain
(chain B). Now assume that due to interactions with chain B,
chain A is elongated in the direction of pulling. This means that
the COM of chain A has moved in the directions of chain B. To
keep the COM of chain A at the same position, the 'rear end' of
chain A has to go in the opposite direction than the 'front end',
so that chain A experiences additional forces and is even more
(and now not due to 'real' interactions, but artificially )
elongated due to the COM fixing. Did I understand that correctly?
Yes.
That's a simple question.
If you keep the COM of a group fixed and part of the group has to
move in one direction, another part of the group will have to
move in another direction.
Berk.
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