[gmx-users] fatty acid monolayer - surface pressure isotherm
Pedro Alexandre Lapido Loureiro
paloureiro at biof.ufrj.br
Thu May 22 21:29:01 CEST 2003
> Greetings all.
> I have a fatty acid monolayer system consisting of 64 arachidic acid
> molecules in vacuum. We are trying to simulate a Langmuir trough
> 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
> the analysis. Once this has been completed I take the resulting gromos
> and use editconf to increase the box vectors so that a packing density of
> 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
> 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
> 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
> 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
> 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?
> 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
> are represented by CH3 and CH2 groups in the GROMACS topology file.
> Periodic boundary conditions are imposed in xyz.
> Thank you,
> Roger McMullen
here are some tips:
-you could increase the simulation length.
-if you are using Berendsen pressure bath, you could increase tau-p.
-you can simulate a bigger monolayer.
-what forcefield are you using?
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica
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