toma0052 wrote:
Hello,
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?
Thanks,
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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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