Re: lipid bilayer MD simulations

From: Thomas Huber <Thomas_Huber_at_Physik.TU-Muenchen.DE>
Date: Wed 7 Mar 2001 19:19:12 +0100 (MET)

Hi Anita, hi community,

there are several forcefields for proteins, nucleic acids, and some other
compounds applicable to biomolecular simulations. All these forcefields
are empirical approximations to the underlying quantummechanical potential
energy hypersurface.
The way these forcefields are generated is different for, e.g. amber or
charmm. The resulting simulations can be tested on the other hand by
comparison with physicochemical data. One has to be careful in application
of the forcefield to a system, since the simulation parameters have also
influence on the result, i.e. a change in the cutoff radius changes the
attractive interaction part of the nonbonded interactions as well as the
electrostatic interactions.
Since the forcefields are sometimes empirically trimmed to give good
result for a certain cutoff/electrostatics/..., changes in these
parameters have to be carefully done. So read the most recent literature
describing the forcefields you want to combine, then you can look, if it
is possible to combine, say amber nucleic acid parameters (I read, this is
a really strong field for amber) with the charmm lipid parameters.
The last comment, or more an open question, I want to give is, that there
might be an effect of simulating with SHAKE on hydrogen atoms involving
bonds, or a fully flexible model. Usually amber and charmm are
parametrized, or I should better say extensively tested, with SHAKE on H
atom involving bonds.


Dr.Thomas Huber University of Arizona
Tel.: (520) 621-2537 Department of Chemistry
FAX: (520) 621-8407 1306 E. University Blvd.
email Tucson, Arizona 85721-0041

On Tue, 6 Mar 2001, Anita Ilze Zvaigzne wrote:

> Dear Dr. Huber:
> > After I changed the LJ parameters to the new CHARMM all-atom lipid force
> > field, the simulations behaved well.
> > I would strongly recommend to use the CHARMM forcefield parameters for
> > lipids (you can switch some compile time options in the amber code to
> > allow for the full CHARMM type forcefield, I can speak only for AMBER 4.1,
> > I haven't got the later versions).
> > It might be possible to combine the CHARMM/lipid and AMBER/protein
> > forcefield, they are not too dissimilar. But there colud be always
> > problems mixing different parametrizations.
> Do you have any idea of why the two forcefields would be so different?
> (Bear with me, I am new at this...)
> Sincerely,
> Anita Zvaigzne
Received on Wed Mar 07 2001 - 10:19:12 PST
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