From: Kay Gottschalk <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
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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