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 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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