Sorry. I simulate DOPG not POPG. Thank you anyway.
On Dec 13, 2007 6:53 PM, Alan Dodd <[EMAIL PROTECTED]> wrote: > 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. > Oh, and read the email you replied to, particularly the bit about 18 > angstroms. > > ----- Original Message ---- > From: Myunggi Yi <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Sent: Thursday, December 13, 2007 6:48:20 PM > Subject: Re: [gmx-users] Gel Phase in DMPC using Berger force field ?? > > I'm running MD at 300 K. > I want fluid phase. > > > On 12/13/07, Myunggi Yi <[EMAIL PROTECTED]> wrote: > > > > Dear Eric, > > > > I'm using Berger force field for DOPG (anionic head group). > > Is is true for DOPG also? > > > > The following is my MD input. > > I'm getting smaller area per lipid (~52 A^2) than expected (~62). > > > > What should I change? > > > > ********************************** > > > > > > ; nblist cut-off > > rlist = 1.6 > > domain-decomposition = no > > > > ; OPTIONS FOR ELECTROSTATICS AND VDW > > ; Method for doing electrostatics > > coulombtype = PME > > rcoulomb-switch = 0 > > rcoulomb = 1.6 > > ; Relative dielectric constant for the medium and the reaction field > > epsilon_r = 1.0 > > epsilon_rf = 1.0 > > ; Method for doing Van der Waals > > vdw-type = Switch > > ; cut-off lengths > > rvdw-switch = 1.2 > > rvdw = 1.4 > > > > ****************************************** > > > > > > On 12/11/07, Eric Jakobsson <[EMAIL PROTECTED] > 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@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 > > > [EMAIL PROTECTED] > > > >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@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 [EMAIL PROTECTED] > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > > > -- > > Best wishes, > > > > MYUNGGI YI > > ================================== > > KLB 419 > > Institute of Molecular Biophysics > > Florida State University > > Tallahassee, FL 32306 > > > > Office: (850) 645-1334 > > http://www.scs.fsu.edu/~myunggi <http://www.scs.fsu.edu/%7Emyunggi> > > > > > -- > Best wishes, > > MYUNGGI YI > ================================== > KLB 419 > Institute of Molecular Biophysics > Florida State University > Tallahassee, FL 32306 > > Office: (850) 645-1334 > http://www.scs.fsu.edu/~myunggi <http://www.scs.fsu.edu/%7Emyunggi> > > > -----Inline Attachment Follows----- > > _______________________________________________ > gmx-users mailing list gmx-users@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. 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