[gmx-users] Gel Phase in DMPC using Berger force field ??

[Eric Jakobsson]

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