[gmx-users] LJ values for a fatty acid
McMullen, Roger L
RMcMullen at ispcorp.com
Mon Feb 2 17:11:02 CET 2004
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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