Hi Eric,
thanks a lot for clarifying this. I suspect that getting a resonable
transition temperature between liquid and gel phase might be rather
challenging...but yes, as you said, would be interesting...
Cheers,
Jochen
Eric Jakobsson wrote:
Several points:
What is called the Berger force field was actually developed by
See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et
al paper tested this force field against another candidate and found
that it was better, and that is the paper that has been cited ever since.
See-Wing did tests of the necessary VDW cut-off for accuracy against
what seemed like the most sensitive test, the value of the dipole
potential at the water-lipid interface, and concluded that one should
use a cut-off of at least 18 angstroms.
The van der Waals parameters for the hydrocarbon tails were
reparameterized in a paper we published a few years ago, and in that
paper we verified that the 18 angstrom cutoff was required for an
accurate liquid hydrocarbon simulation also.
Recently See-Wing has reparameterized the van der Waals parameters in
the lipid head groups, using specific volumes of liquids comprised of
small molecules that are part of the head group. The resulting force
fields, which retain the partial charges of the Berger-Chiu field,
work very well in replicating x-ray structure factors of lipids with
various chain compositions, but he has not yet tried to do gel
phase--that would be interesting. The journal ms. is still sitting on
my desk, I am afraid, but there is a pretty good description of the
parameterization in a chapter in a book that Scott Feller is editing,
which we can send on request, as well as the lipid complete force
field in itself. We believe it is state of the art at this time.
Best,
Eric
At 10:22 AM 12/11/2007, you wrote:
Hi Steffen,
thanks a lot for your reply.
-what are your VdW cutoffs? Berger lipids absolutely need the
0.8/1.4 nm
twin range cutoff for working properly. Are you using PME for
electrostatics?
I used a LJ-cutoff at 1.0nm. That's what was used for the original
Berger-Paper (*O Berger, O Edholm and F Jähnig, */Biophysical
Journal/ 72: 2002-2013 (1997). Shouldn't this be all right?
And I used PME (which was indeed not used in the original work.
-how did you set up the pressure coupling?
I used weak coupling (tau=1.0ps)
-900 waters are not really much, the head groups will probably interact
with their mirror images due to pbc. Try a lot more (thought about
10000?) for having a "real" bilayer in a solution.
I also tried with more water, the gel phase did not appear either.
>From my experience, the Berger lipids are well defined for a specific
temperature, but if you go up/down the temperature scale, they are not
really following the experimental values/phase behaviour. By the way:
experimental data on lipid order parameters varies considerably
throughout the complete literature, so don't rely onto that too much as
well.
Sorry for giving more questions than answers, but that's the shitty
part
with lipid bilayers in MD...
Steffen
Thanks again,
Jochen
--
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************
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---------------------------------
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of
Biochemistry, and of the Center for Biophysics and Computational Biology
Senior Research Scientist, National Center for Supercomputing
Applications
Professor, Beckman Institute for Advanced Science and Technology
3261 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896 Fax 217 244 9757
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************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************
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