[gmx-users] center of mass pulling in AFM

Kay Gottschalk kay.gottschalk at physik.uni-muenchen.de
Tue Jul 18 16:07:19 CEST 2006

Thanks for your suggestion to do something more similar to reality.  
We are trying to mimick an experiment with covalently bound protein.  
Of course the protein is not fixed in the center of mass, but at some  
sidechain. Now due to all kind of effects, if we simulate with this  
sidechain atom fixed, the protein unfolds. This is mainly caused by  
the sad fact that our simulations still cannot span the time scale of  
the experiment. Too bad. Therefore, we need to find some way around  
this problem. Since the unfolding has something to do with a  
combination of force propagation and viscous drag, it might be more  
similar to the experiment to pull at the center of mass than at one  
atom. This is when our discussion about COM started. You see, we are  
indeed trying to simulate something more similar to reality.
Thanks again for your comments,

On Jul 18, 2006, at 3:39 PM, 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: Re: [gmx-users] center of mass pulling in AFM
>> Date: Tue, 18 Jul 2006 14:41:53 +0200
>> 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?
> Indeed.
> But fixing a single atom is space is quite an unrealistic
> situation, unless you are trying to mimick something like
> an experiment where a protein is covalently bound
> to a surface.
> It all depends on what you want to do.
> There is probably some kind of experiment or biological
> process that you are trying to mimick.
> Doing something more similar to reality should reduce
> your problems.
> Berk.
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