[gmx-users] center of mass pulling in AFM

[Berk Hess]

>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.