[gmx-users] fatty acid monolayer - pressure vs. area
McMullen, Roger L
RMcMullen at ispcorp.com
Thu May 22 02:43:01 CEST 2003
I have a fatty acid monolayer system consisting of 64 arachidic acid
molecules in vacuum. We are trying to simulate a Langmuir trough experiment
in which the lateral pressure is monitored as a function of the packing
density. The x and y vectors of the box are initially set at values that
provide a monolayer packing density of 18.5 A^2/molecule.
At this packing density, I first perform a MD simulation for 1000 ps with
position restraints on all atoms. This is followed by another 1000 ps
simulation in which the acid headgroups are position restrained while the
aliphatic chains are not. I then execute a 2000 ps simulation without
restraints to allow equilibration followed by another 2000 ps simulation for
the analysis. Once this has been completed I take the resulting gromos file
and use editconf to increase the box vectors so that a packing density of 19
A^2/molecule is obtained. Similar to the case of 18.5 A^2/molecule, a 2000
ps equilibration MD run is completed for the 19 A^2/molecule system followed
by another 2000 ps simulation for analysis. The resulting gromos file from
the second 2000 ps run for the 19 A^2/molecule system is then used via
editconf to generate a box size yielding a packing density of 19.5
A^2/molecule. Again, a 2000 ps equilibration simulation is conducted
followed by a 2000 ps analysis run. This process is continued up to 25
As you probably expect, I am trying to generate a Pi-A (surface pressure vs.
area) isotherm by manipulating the area per molecule and monitoring the
pressure. The problem I have encountered is that the diagonal pressure
values (Pres-XX, Pres-YY, and Pres-ZZ) fluctuate quite drastically from one
simulation at a given area per molecule to another. For example when going
from 18.5 to 19 A^2/molecule, I see an increase rather a decrease in the
diagonal pressure elements. When going from 19 to 19.5 A^2/molecule I
observe a decrease in pressure followed by an increase from 19.5 to 20
A^2/molecule. This occurs at all packing densities up to 25 A^2/molecule.
The work described above, as noted, was performed in vacuum. There has been
some work cited in the literature in which an entire Pi-A diagram was
obtained for a fatty acid monolayer. Their system was in vacuum, however,
they utilized a modified LJ potential in a plane just below the headgroups
to simulate the interaction of the fatty acids with water (something my
system is missing). Alternatively, I have also looked at work by Alhstrom
and Berendsen who simulated a lecithin monolayer (using a dual monolayer
system) and monitored the surface pressure at a specified packing density
which agreed quite well with experiments. They employed a dual monolayer
system with a layer of water in between the two monolayers (This was done to
provide periodic boundary conditions in z). I am in the process of
conducting similar simulations, however, I first wanted to see if it is
possible to find any success with a system in vacuum.
Finally, to the question. Does anyone have any tips or suggestions? Below,
I have provided some of the system parameters in the event that anyone is
interested. For example, I only generate velocities and have a constrained
start in the initial position restrained simulation. The length of the box
in the z-direction is 7.5 nm (fatty acid length = 2.6 nm) so that the
headgroups do not interact with the chains. The methyl and methylene groups
are represented by CH3 and CH2 groups in the GROMACS topology file.
Periodic boundary conditions are imposed in xyz.
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