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<DIV><FONT face=Arial color=#0000ff size=2><SPAN class=620432517-03022004>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.?</SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=620432517-03022004></SPAN></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=620432517-03022004>Thanks,</SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=620432517-03022004>Roger</SPAN></FONT></DIV>
<BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px">
<DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma
size=2>-----Original Message-----<BR><B>From:</B> Eric Jakobsson
[mailto:jake@ncsa.uiuc.edu]<BR><B>Sent:</B> Monday, February 02, 2004 11:28
PM<BR><B>To:</B> gmx-users@gromacs.org<BR><B>Subject:</B> Re: [gmx-users] LJ
values for a fatty acid<BR><BR></FONT></DIV>Did you use the hydrocarbon
parameters in <BR><BR><FONT face="Times, Times">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. <I>J. Phys. Chem. </FONT><FONT
face="MS Serif, Geneva">B </I>103:6323-6327<BR><BR></FONT>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>Eric
<BR><BR>At 11:09 AM 2/2/2004 -0500, you wrote:<BR>
<BLOCKQUOTE class=cite cite="" type="cite">Hi all.<BR><BR>I am simulating a
monolayer system of eicosanoic acid (arachidic acid) on<BR>SPC water.
We are trying to simulate a Langmuir trough experiment in which<BR>lateral
pressure is monitored as a function of the molecular packing
density<BR>(perimeter area). I have tried to use several different
united atoms for<BR>the hydrocarbon tails, however, the resulting Pi-A
diagram is always shifted<BR>to higher packing densities (e.g. from 18.5
A^2/molecule to 17.5<BR>A^2/molecule) in each case. The shift in
the Pi-A diagram is not feasible<BR>as the cross-sectional area of the fatty
is 18.5 A^2/molecule. Below are<BR>three of the systems.<BR><BR>System
1: GMX forcefield with CH2 and CH3 united atoms.<BR>System 2:
GMX forcefield with CP2 and CP3 united atoms.<BR>System 3: GMX
forcefield with LP2 and LP3 united atoms.<BR><BR>My suspicion is that the
shift in the Pi-A diagram has less to do with the<BR>tail interactions (in
this case) and more to do with the headgroup<BR>interactions. Does
this occur because I am using the GMX carbonyl carbon,<BR>GMX carbonyl
oxygen, GMX carboxyl oxygen, and GMX hydrogen for the
headgroup<BR>atoms? My headgroup has no net charge, but the headgroup
atoms have the<BR>same partial charges as the lauroic acid topology file
provided with the<BR>distribution. I have plotted the LJ potentials of
the tail atoms and<BR>headgroup atoms for the above three systems as well as
for the ffOPLS and<BR>ffG43a2 forcefields. It does not seem that the
headgroup atoms for ffOPLS<BR>and ffG43a2 are drastically different.
Do I need to parameterize headgroup<BR>atoms for this particular
application? If so, does anyone have
any<BR>suggestions?<BR><BR>Thanks,<BR>Roger
McMullen<BR><BR><BR>_______________________________________________<BR>gmx-users
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send it to gmx-users-request@gromacs.org.</BLOCKQUOTE><X-SIGSEP>
<P></X-SIGSEP>---------------------------------<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></P></BLOCKQUOTE></BODY></HTML>