[gmx-users] Surface Tension of a lipid bilayer
David van der Spoel
spoel at xray.bmc.uu.se
Sat Dec 2 10:22:21 CET 2006
> I have a question about calculating the surface tension for the
> water-lipid interface of a lipid bilayer. After an MD run, I can use my .edr
> file and g_energy to calculate the surface tension. I believe that the
> surface tension is calculated something like gamma = (Pzz-(Pxx+Pyy)/2)/L. I
> was wondering though, is the pressure tensor and hence surface tension
> calculated over the entire simulation box? I would assume so, since I did
> not specify any molecules. To find the water-lipid surface tension, would I
> not need to sum over only the molecules at the surface? Would this be
> do-able in Gromacs? Would I have to write something separate to do this?
> In my coordinate file, I have DPPC atoms, solvent atoms, and other atoms
> (those that make up the head group ie O,N etc.). Could I just make an index
> group that is not DPPC and not Solvent, and sum over those atoms?
> Mike Tomasini
First, one usually has two interfaces, in which case you have to divide
the surface tension by two. This is computed over the entire box but it
will give you a perfectly good result.
Further it would be interesting to calculate local pressures, and there
is an ancient gromacs version that does this (can be downloaded from the
website). The reason this is not in standard gromacs is that it is quite
expensive to compute.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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