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

[Zoltan Varga]

Dear all,

For the gel-to-liquid crystalline phase transition in DPPC and DPPE there is a paper:
Leekumjorn and Sum, BBA, 1768 (2007) 354-365
I've found it several month ago and I haven't red through it completely, but they used the Berger force field.

Best,
Zoltan

Eric Jakobsson <jake at ncsa.uiuc.edu> wrote: Yes, this should be attempted.  Perhaps the 
ultimate test of a force field is to nail a phase change.

At 03:34 AM 12/12/2007, you wrote:
>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
>>>************************************************
>>>_______________________________________________
>>>gmx-users mailing list    gmx-users at gromacs.org
>>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>>Please search the archive at http://www.gromacs.org/search before posting!
>>>Please don't post (un)subscribe requests to 
>>>the list. Use the www interface or send it to gmx-users-request at gromacs.org.
>>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>---------------------------------
>>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
>>
>>
>>
>>
>>_______________________________________________
>>gmx-users mailing list    gmx-users at gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before posting!
>>Please don't post (un)subscribe requests to the 
>>list. Use the www interface or send it to gmx-users-request at gromacs.org.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>.
>
>
>--
>************************************************
>Jochen Hub
>Max Planck Institute for Biophysical Chemistry
>Computational biomolecular dynamics group
>Am Fassberg 11
>D-37077 Goettingen, Germany
>Email: jhub[at]gwdg.de
>************************************************
>_______________________________________________
>gmx-users mailing list    gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please search the archive at http://www.gromacs.org/search before posting!
>Please don't post (un)subscribe requests to the 
>list. Use the www interface or send it to gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php

---------------------------------
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




_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


       
---------------------------------
Looking for last minute shopping deals?  Find them fast with Yahoo! Search.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071212/5069ea6b/attachment.html>