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,
Kay.
On Jul 18, 2006, at 3:39 PM, Berk Hess wrote:
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 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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