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

Fri Dec 14 00:53:59 CET 2007

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 

-- 
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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