<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">What topology are you using? If you're using one based on the Kartunnen's group POPG (the only publicly available one I know of), then be aware that I think they saw gel phase too.</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Oh, and read the email you replied to, particularly the bit about 18 angstroms.<BR><BR></DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">----- Original Message ----<BR>From: Myunggi Yi <myunggi@gmail.com><BR>To: Discussion list for GROMACS users <gmx-users@gromacs.org><BR>Sent: Thursday, December 13, 2007 6:48:20 PM<BR>Subject: Re: [gmx-users] Gel Phase in DMPC using Berger force field ??<BR><BR>
<DIV>I'm running MD at 300 K.</DIV>
<DIV>I want fluid phase.<BR><BR> </DIV>
<DIV><SPAN class=gmail_quote>On 12/13/07, <B class=gmail_sendername>Myunggi Yi</B> <<A href="mailto:myunggi@gmail.com" target=_blank rel=nofollow ymailto="mailto:myunggi@gmail.com">myunggi@gmail.com</A>> wrote:</SPAN>
<BLOCKQUOTE class=gmail_quote style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<DIV>Dear Eric,</DIV>
<DIV> </DIV>
<DIV>I'm using Berger force field for DOPG (anionic head group).</DIV>
<DIV>Is is true for DOPG also?</DIV>
<DIV> </DIV>
<DIV>The following is my MD input.</DIV>
<DIV>I'm getting smaller area per lipid (~52 A^2) than expected (~62).</DIV>
<DIV> </DIV>
<DIV>What should I change?</DIV>
<DIV> </DIV>
<DIV>**********************************<BR> </DIV>
<P>; nblist cut-off <BR>rlist = 1.6<BR>domain-decomposition = no</P>
<P>; OPTIONS FOR ELECTROSTATICS AND VDW<BR>; Method for doing electrostatics<BR>coulombtype = PME<BR>rcoulomb-switch = 0<BR>rcoulomb = 1.6<BR>; Relative dielectric constant for the medium and the reaction field <BR>epsilon_r = 1.0<BR>epsilon_rf = 1.0<BR>; Method for doing Van der Waals<BR>vdw-type = Switch<BR>; cut-off lengths<BR>rvdw-switch =
1.2<BR>rvdw = 1.4<BR></P>
<P>******************************************</P>
<DIV><SPAN class=e id=q_116d4d4efef1c3c7_1>
<DIV><BR> </DIV>
<DIV><SPAN class=gmail_quote>On 12/11/07, <B class=gmail_sendername>Eric Jakobsson</B> <<A href="mailto:jake@ncsa.uiuc.edu" target=_blank rel=nofollow ymailto="mailto:jake@ncsa.uiuc.edu">jake@ncsa.uiuc.edu </A>> wrote:</SPAN>
<BLOCKQUOTE class=gmail_quote style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">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 al<BR>paper tested this force field against another<BR>candidate and found that it was better, and that<BR>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 potential<BR>at the water-lipid interface, and concluded that<BR>one should use a cut-off of at least 18 angstroms.<BR><BR>The van der Waals parameters for the hydrocarbon <BR>tails were reparameterized in a paper we<BR>published a few years ago, and in that paper we<BR>verified that the 18 angstrom cutoff was required<BR>for an accurate liquid hydrocarbon simulation
also.<BR><BR>Recently See-Wing has reparameterized the van der <BR>Waals parameters in the lipid head groups, using<BR>specific volumes of liquids comprised of small<BR>molecules that are part of the head group. The<BR>resulting force fields, which retain the partial<BR>charges of the Berger-Chiu field, work very well <BR>in replicating x-ray structure factors of lipids<BR>with various chain compositions, but he has not<BR>yet tried to do gel phase--that would be<BR>interesting. The journal ms. is still sitting on<BR>my desk, I am afraid, but there is a pretty good <BR>description of the parameterization in a chapter<BR>in a book that Scott Feller is editing, which we<BR>can send on request, as well as the lipid<BR>complete force field in itself. We believe it is<BR>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>>><BR>>I used a LJ-cutoff at 1.0nm. That's what was<BR>>used for the original Berger-Paper (*O Berger, O<BR>>Edholm and F Jähnig, */Biophysical Journal/ 72:<BR>>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>>><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>>><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>>><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]<A href="http://gwdg.de/"
target=_blank>gwdg.de</A><BR>>************************************************<BR>>_______________________________________________ <BR>>gmx-users mailing list <A href="mailto:gmx-users@gromacs.org" target=_blank rel=nofollow ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>><A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target=_blank rel=nofollow> http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>>Please search the archive at <A href="http://www.gromacs.org/search" target=_blank rel=nofollow>http://www.gromacs.org/search </A>before posting!<BR>>Please don't post (un)subscribe requests to the<BR>>list. Use the www interface or send it to <A href="mailto:gmx-users-request@gromacs.org" target=_blank rel=nofollow ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>>Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php"
target=_blank rel=nofollow>http://www.gromacs.org/mailing_lists/users.php </A><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 <A href="mailto:gmx-users@gromacs.org" target=_blank rel=nofollow ymailto="mailto:gmx-users@gromacs.org"> gmx-users@gromacs.org</A><BR><A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target=_blank
rel=nofollow>http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/search" target=_blank rel=nofollow>http://www.gromacs.org/search</A> before posting!<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to <A href="mailto:gmx-users-request@gromacs.org" target=_blank rel=nofollow ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php" target=_blank rel=nofollow>http://www.gromacs.org/mailing_lists/users.php</A><BR></BLOCKQUOTE></DIV><BR><BR clear=all><BR></SPAN></DIV>-- <BR>Best wishes, <BR><BR>MYUNGGI YI<BR>==================================<BR>KLB 419<BR>Institute of Molecular Biophysics <BR>Florida State University<BR>Tallahassee, FL 32306<BR><BR>Office: (850) 645-1334<BR><A href="http://www.scs.fsu.edu/~myunggi" target=_blank
rel=nofollow>http://www.scs.fsu.edu/~myunggi </A></BLOCKQUOTE></DIV><BR><BR clear=all><BR>-- <BR>Best wishes,<BR><BR>MYUNGGI YI<BR>==================================<BR>KLB 419<BR>Institute of Molecular Biophysics<BR>Florida State University<BR>Tallahassee, FL 32306 <BR><BR>Office: (850) 645-1334<BR><A href="http://www.scs.fsu.edu/~myunggi" target=_blank rel=nofollow>http://www.scs.fsu.edu/~myunggi</A><!-- kill -->
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