[gmx-users] Gel Phase in DMPC using Berger force field ??
Myunggi Yi
myunggi at gmail.com
Fri Dec 14 15:03:02 CET 2007
Sorry.
I simulate DOPG not POPG.
Thank you anyway.
On Dec 13, 2007 6:53 PM, Alan Dodd <anoddlad at yahoo.com> 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 <myunggi at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at 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 <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
> > > >************************************************
> > > >_______________________________________________
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> > >
> > > ---------------------------------
> > > 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
> > >
> > >
> > >
> > >
> > > _______________________________________________
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> >
> >
> >
> > --
> > 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>
>
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--
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
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