Dear all,<br><br>For the gel-to-liquid crystalline phase transition in DPPC and DPPE there is a paper:<br>Leekumjorn and Sum, BBA, 1768 (2007) 354-365<br>I've found it several month ago and I haven't red through it completely, but they used the Berger force field.<br><br>Best,<br>Zoltan<br><br><b><i>Eric Jakobsson <jake@ncsa.uiuc.edu></i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> Yes, this should be attempted. Perhaps the <br>ultimate test of a force field is to nail a phase change.<br><br>At 03:34 AM 12/12/2007, you wrote:<br>>Hi Eric,<br>><br>>thanks a lot for clarifying this. I suspect that <br>>getting a resonable transition temperature <br>>between liquid and gel phase might be rather <br>>challenging...but yes, as you said, would be interesting...<br>><br>>Cheers,<br>>Jochen<br>><br>><br>>Eric Jakobsson wrote:<br>>>Several
points:<br>>><br>>>What is called the Berger force field was <br>>>actually developed by See-Wing Chiu in our lab <br>>>and presented in a 1995 paper. The Berger et <br>>>al paper tested this force field against <br>>>another candidate and found that it was better, <br>>>and that is the paper that has been cited ever since.<br>>><br>>>See-Wing did tests of the necessary VDW cut-off <br>>>for accuracy against what seemed like the most <br>>>sensitive test, the value of the dipole <br>>>potential at the water-lipid interface, and <br>>>concluded that one should use a cut-off of at least 18 angstroms.<br>>><br>>>The van der Waals parameters for the <br>>>hydrocarbon tails were reparameterized in a <br>>>paper we published a few years ago, and in that <br>>>paper we verified that the 18 angstrom cutoff <br>>>was required for an accurate liquid hydrocarbon
simulation also.<br>>><br>>>Recently See-Wing has reparameterized the van <br>>>der Waals parameters in the lipid head groups, <br>>>using specific volumes of liquids comprised of <br>>>small molecules that are part of the head <br>>>group. The resulting force fields, which <br>>>retain the partial charges of the Berger-Chiu <br>>>field, work very well in replicating x-ray <br>>>structure factors of lipids with various chain <br>>>compositions, but he has not yet tried to do <br>>>gel phase--that would be interesting. The <br>>>journal ms. is still sitting on my desk, I am <br>>>afraid, but there is a pretty good description <br>>>of the parameterization in a chapter in a book <br>>>that Scott Feller is editing, which we can send <br>>>on request, as well as the lipid complete force <br>>>field in itself. We believe it is state of the art at this
time.<br>>><br>>>Best,<br>>>Eric<br>>>At 10:22 AM 12/11/2007, you wrote:<br>>>>Hi Steffen,<br>>>><br>>>>thanks a lot for your reply.<br>>>>>-what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm<br>>>>>twin range cutoff for working properly. Are you using PME for<br>>>>>electrostatics?<br>>>>I used a LJ-cutoff at 1.0nm. That's what was <br>>>>used for the original Berger-Paper (*O Berger, <br>>>>O Edholm and F Jähnig, */Biophysical Journal/ <br>>>>72: 2002-2013 (1997). Shouldn't this be all right?<br>>>><br>>>>And I used PME (which was indeed not used in the original work.<br>>>><br>>>>>-how did you set up the pressure coupling?<br>>>>I used weak coupling (tau=1.0ps)<br>>>><br>>>>>-900 waters are not really much, the head groups will probably
interact<br>>>>>with their mirror images due to pbc. Try a lot more (thought about<br>>>>>10000?) for having a "real" bilayer in a solution.<br>>>>I also tried with more water, the gel phase did not appear either.<br>>>><br>>>>> >From my experience, the Berger lipids are well defined for a specific<br>>>>>temperature, but if you go up/down the temperature scale, they are not<br>>>>>really following the experimental values/phase behaviour. By the way:<br>>>>>experimental data on lipid order parameters varies considerably<br>>>>>throughout the complete literature, so don't rely onto that too much as<br>>>>>well.<br>>>>>Sorry for giving more questions than answers, but that's the shitty part<br>>>>>with lipid bilayers in MD...<br>>>>>Steffen<br>>>>Thanks
again,<br>>>>Jochen<br>>>><br>>>><br>>>><br>>>>--<br>>>>************************************************<br>>>>Jochen Hub<br>>>>Max Planck Institute for Biophysical Chemistry<br>>>>Computational biomolecular dynamics group<br>>>>Am Fassberg 11<br>>>>D-37077 Goettingen, Germany<br>>>>Email: jhub[at]gwdg.de<br>>>>************************************************<br>>>>_______________________________________________<br>>>>gmx-users mailing list gmx-users@gromacs.org<br>>>>http://www.gromacs.org/mailman/listinfo/gmx-users<br>>>>Please search the archive at http://www.gromacs.org/search before posting!<br>>>>Please don't post (un)subscribe requests to <br>>>>the list. Use the www interface or send it to gmx-users-request@gromacs.org.<br>>>>Can't post? Read
http://www.gromacs.org/mailing_lists/users.php<br>>><br>>>---------------------------------<br>>>Eric Jakobsson, Ph.D.<br>>>Professor, Department of Molecular and <br>>>Integrative Physiology, and of Biochemistry, <br>>>and of the Center for Biophysics and Computational Biology<br>>>Senior Research Scientist, National Center for Supercomputing Applications<br>>>Professor, Beckman Institute for Advanced Science and Technology<br>>>3261 Beckman Institute, mc251<br>>>University of Illinois, Urbana, IL 61801<br>>>ph. 217-244-2896 Fax 217 244 9757<br>>><br>>><br>>><br>>><br>>>_______________________________________________<br>>>gmx-users mailing list gmx-users@gromacs.org<br>>>http://www.gromacs.org/mailman/listinfo/gmx-users<br>>>Please search the archive at http://www.gromacs.org/search before posting!<br>>>Please don't post (un)subscribe requests to the
<br>>>list. Use the www interface or send it to gmx-users-request@gromacs.org.<br>>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>>><br>>>.<br>><br>><br>>--<br>>************************************************<br>>Jochen Hub<br>>Max Planck Institute for Biophysical Chemistry<br>>Computational biomolecular dynamics group<br>>Am Fassberg 11<br>>D-37077 Goettingen, Germany<br>>Email: jhub[at]gwdg.de<br>>************************************************<br>>_______________________________________________<br>>gmx-users mailing list gmx-users@gromacs.org<br>>http://www.gromacs.org/mailman/listinfo/gmx-users<br>>Please search the archive at http://www.gromacs.org/search before posting!<br>>Please don't post (un)subscribe requests to the <br>>list. Use the www interface or send it to gmx-users-request@gromacs.org.<br>>Can't post? Read
http://www.gromacs.org/mailing_lists/users.php<br><br>---------------------------------<br>Eric Jakobsson, Ph.D.<br>Professor, Department of Molecular and <br>Integrative Physiology, and of Biochemistry, and <br>of the Center for Biophysics and Computational Biology<br>Senior Research Scientist, National Center for Supercomputing Applications<br>Professor, Beckman Institute for Advanced Science and Technology<br>3261 Beckman Institute, mc251<br>University of Illinois, Urbana, IL 61801<br>ph. 217-244-2896 Fax 217 244 9757<br><br><br><br><br>_______________________________________________<br>gmx-users mailing list gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read
http://www.gromacs.org/mailing_lists/users.php<br></blockquote><br><p> 
<hr size=1>Looking for last minute shopping deals? <a href="http://us.rd.yahoo.com/evt=51734/*http://tools.search.yahoo.com/newsearch/category.php?category=shopping">
Find them fast with Yahoo! Search.</a>