[gmx-users] center of mass pulling in AFM

Kay Gottschalk kay.gottschalk at physik.uni-muenchen.de
Tue Jul 18 12:44:20 CEST 2006

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?

On Jul 18, 2006, at 11:31 AM, Berk Hess wrote:

>> From: Kay Gottschalk <kay.gottschalk at physik.uni-muenchen.de>
>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Subject: [gmx-users] center of mass pulling in AFM
>> Date: Mon, 17 Jul 2006 12:58:02 +0200
>> Hi there,
>> we are doing pulling simulations of protein complexes. For these   
>> simulations, we keep the COM of one group fixed and pull on the  
>> COM  of the other group. Now we got into this discussion, whether  
>> this  introduces artificial distortions on the hold protein. If  
>> the protein  deforms into the direction of the force vector, the  
>> center of mass  changes. Does this mean that a force on the other  
>> end of the protein  is applied, so that the other end also deforms  
>> in order to keep the  center of mass fixed? Or how is the COM held  
>> fixed ?
> This all depends on what you are keeping fixed.
> Of which groups are you keeping the COM fixed?
> Since MD preserves momenta, you can only
> fix distances between COMs by adding forces,
> which is exactly what the pull code does.
> Additionally fixing more than one COM will
> introduce additional forces.
> Berk.
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