[gmx-users] Gel Phase in DMPC using Berger force field ??
jake at ncsa.uiuc.edu
Wed Dec 12 02:08:34 CET 2007
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.
At 10:22 AM 12/11/2007, you wrote:
>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
>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
>>Sorry for giving more questions than answers, but that's the shitty part
>>with lipid bilayers in MD...
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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
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