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

[Jochen Hub]

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
************************************************