[gmx-users] Surface Tension of a lipid bilayer
toma0052 at umn.edu
Fri Dec 1 23:59:20 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?
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