[gmx-users] LJ values for a fatty acid
McMullen, Roger L
RMcMullen at ispcorp.com
Tue Feb 3 18:40:01 CET 2004
Thanks a lot Eric. I'm going to try the LJ parameters from the paper. This
may seem like a silly question, but how much influence do the LJ parameters
of the headgroup atoms play in the molecular volume of a monolayer (or
bilayer) in a box. I would have suspected that they play a big role,
however, it seems that most attention is given to the parameters of the
methylene and methyl united atoms. Is this because the headgroup atoms are
not united atoms and should behave the same in most environments. e.g.
proteins, bilayers, monolayers, etc.?
From: Eric Jakobsson [mailto:jake at ncsa.uiuc.edu]
Sent: Monday, February 02, 2004 11:28 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] LJ values for a fatty acid
Did you use the hydrocarbon parameters in
Chiu, S. W., Clark, M. M., Jakobsson, E., Subramaniam, S., and H. L. Scott.
1999b. Optimizations of hydrocarbon chain interaction parameters:
Application to the simulation of fluid phase lipid bilayers. J. Phys. Chem.
I think these are the right united atom parameters because they match the
specific volume of the fluid hydrocarbons over all chain lengths, and that
provides just the right number of constraints to determine the parameters
At 11:09 AM 2/2/2004 -0500, you wrote:
I am simulating a monolayer system of eicosanoic acid (arachidic acid) on
SPC water. We are trying to simulate a Langmuir trough experiment in which
lateral pressure is monitored as a function of the molecular packing density
(perimeter area). I have tried to use several different united atoms for
the hydrocarbon tails, however, the resulting Pi-A diagram is always shifted
to higher packing densities (e.g. from 18.5 A^2/molecule to 17.5
A^2/molecule) in each case. The shift in the Pi-A diagram is not feasible
as the cross-sectional area of the fatty is 18.5 A^2/molecule. Below are
three of the systems.
System 1: GMX forcefield with CH2 and CH3 united atoms.
System 2: GMX forcefield with CP2 and CP3 united atoms.
System 3: GMX forcefield with LP2 and LP3 united atoms.
My suspicion is that the shift in the Pi-A diagram has less to do with the
tail interactions (in this case) and more to do with the headgroup
interactions. Does this occur because I am using the GMX carbonyl carbon,
GMX carbonyl oxygen, GMX carboxyl oxygen, and GMX hydrogen for the headgroup
atoms? My headgroup has no net charge, but the headgroup atoms have the
same partial charges as the lauroic acid topology file provided with the
distribution. I have plotted the LJ potentials of the tail atoms and
headgroup atoms for the above three systems as well as for the ffOPLS and
ffG43a2 forcefields. It does not seem that the headgroup atoms for ffOPLS
and ffG43a2 are drastically different. Do I need to parameterize headgroup
atoms for this particular application? If so, does anyone have any
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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
405 N. Mathews Avenue
University of Illinois, Urbana, IL 61801
ph. 217-244-2896 fax 217-244-2909
(Currently on leave to NIH to serve as Director of Center for Bioinformatics
and Computational Biology at the National Institute of General Medical
Sciences and Chair of the NIH Biomedical Information Science and Technology
Initiative Consortium. Usual schedule is four days a week at NIH and three
days a week at Illlinois.)
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