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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.<br><br>
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 directly.<br><br>
Eric <br><br>
At 12:38 PM 2/3/2004 -0500, you wrote:<br>
<blockquote type=cite class=cite cite><font face="arial" size=2 color="#0000FF">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.?</font><br>
<br>
<font face="arial" size=2 color="#0000FF">Thanks,</font><br>
<font face="arial" size=2 color="#0000FF">Roger</font>
<dl><font face="tahoma" size=2>
<dd>-----Original Message-----
<dd>From:</b> Eric Jakobsson
[<a href="mailto:jake@ncsa.uiuc.edu" eudora="autourl">mailto:jake@ncsa.uiuc.edu</a>]
<dd>Sent:</b> Monday, February 02, 2004 11:28 PM
<dd>To:</b> gmx-users@gromacs.org
<dd>Subject:</b> Re: [gmx-users] LJ values for a fatty acid<br><br>
</font>
<dd>Did you use the hydrocarbon parameters in <br><br>
<font face="Times, Times">
<dd>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. </font><font face="MS Serif, Geneva">B
</i>103:6323-6327<br><br>
</font>
<dd>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 unambiguously.<br><br>
<dd>Eric <br><br>
<dd>At 11:09 AM 2/2/2004 -0500, you
wrote:<blockquote type=cite class=cite cite>
<dd>Hi all.<br><br>
<dd>I am simulating a monolayer system of eicosanoic acid (arachidic
acid) on
<dd>SPC water. We are trying to simulate a Langmuir trough
experiment in which
<dd>lateral pressure is monitored as a function of the molecular packing
density
<dd>(perimeter area). I have tried to use several different united
atoms for
<dd>the hydrocarbon tails, however, the resulting Pi-A diagram is always
shifted
<dd>to higher packing densities (e.g. from 18.5 A^2/molecule to 17.5
<dd>A^2/molecule) in each case. The shift in the Pi-A diagram
is not feasible
<dd>as the cross-sectional area of the fatty is 18.5 A^2/molecule.
Below are
<dd>three of the systems.<br><br>
<dd>System 1: GMX forcefield with CH2 and CH3 united atoms.
<dd>System 2: GMX forcefield with CP2 and CP3 united atoms.
<dd>System 3: GMX forcefield with LP2 and LP3 united
atoms.<br><br>
<dd>My suspicion is that the shift in the Pi-A diagram has less to do
with the
<dd>tail interactions (in this case) and more to do with the headgroup
<dd>interactions. Does this occur because I am using the GMX
carbonyl carbon,
<dd>GMX carbonyl oxygen, GMX carboxyl oxygen, and GMX hydrogen for the
headgroup
<dd>atoms? My headgroup has no net charge, but the headgroup atoms
have the
<dd>same partial charges as the lauroic acid topology file provided with
the
<dd>distribution. I have plotted the LJ potentials of the tail
atoms and
<dd>headgroup atoms for the above three systems as well as for the ffOPLS
and
<dd>ffG43a2 forcefields. It does not seem that the headgroup atoms
for ffOPLS
<dd>and ffG43a2 are drastically different. Do I need to
parameterize headgroup
<dd>atoms for this particular application? If so, does anyone have
any
<dd>suggestions?<br><br>
<dd>Thanks,
<dd>Roger McMullen<br><br>
<br><br>
<dd>_______________________________________________
<dd>gmx-users mailing list
<dd>gmx-users@gromacs.org
<dd><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" eudora="autourl">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
<dd>Please don't post (un)subscribe requests to the list. Use the
<dd>www interface or send it to
gmx-users-request@gromacs.org.</blockquote>
<dd>---------------------------------
<dd>Eric Jakobsson, Ph.D.
<dd>Professor, Department of Molecular and Integrative Physiology, and of
Biochemistry
<dd>Senior Research Scientist, National Center for Supercomputing
Applications
<dd>Professor, Beckman Institute for Advanced Science and Technology
<dd>4021 Beckman Institute, mc251
<dd>405 N. Mathews Avenue
<dd>University of Illinois, Urbana, IL 61801
<dd>ph. 217-244-2896 fax
217-244-2909<br><br>
<dd>(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.)<br><br>
</blockquote>
<x-sigsep><p></x-sigsep>
</dl>---------------------------------<br>
Eric Jakobsson, Ph.D.<br>
Professor, Department of Molecular and Integrative Physiology, and of
Biochemistry<br>
Senior Research Scientist, National Center for Supercomputing
Applications<br>
Professor, Beckman Institute for Advanced Science and Technology<br>
4021 Beckman Institute, mc251<br>
405 N. Mathews Avenue<br>
University of Illinois, Urbana, IL 61801<br>
ph. 217-244-2896 fax
217-244-2909<br><br>
(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.)<br><br>
<br>
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