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

Myunggi Yi myunggi at gmail.com
Thu Dec 13 19:48:20 CET 2007


I'm running MD at 300 K.
I want fluid phase.


On 12/13/07, Myunggi Yi <myunggi at gmail.com> 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 <jake at ncsa.uiuc.edu > 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
> >
>
>
>
> --
> 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




-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071213/2fbbeecb/attachment.html>


More information about the gromacs.org_gmx-users mailing list