[gmx-users] LJ values for a fatty acid
jake at ncsa.uiuc.edu
Sun Feb 8 22:56:01 CET 2004
The headgroup atoms have some influence as well. We writing up some work
on that. Essentially we find our best results from the OPLS van der Waals
LJ combined with our own ab initio calculations for the partial charges.
I am copying See-Wing Chiu in our group who has been working on revising
and validating the head group parameters, so that if you have some detailed
questions on what are the best parameters to use there, you can ask him
At 12:38 PM 2/3/2004 -0500, you wrote:
>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. B 103:6323-6327
>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.)
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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