Re: [gmx-users] Surface Tension of a lipid bilayer

2006-12-02 Thread Eric Jakobsson 
The theory underlying this is reviewed in our group's 1995 
Biophysical Journal (Chiu et al) paper where we introduced the 
surface tension boundary conditions---a deeper look at the theory is 
in in Steve White's earlier paper in PNAS that is referenced in our 
'95 paper.  The short answer is yes, you include all the atoms in the 
system.  That reflects the fact that the surface tension, as measured 
in a laboratory, is a property of the entire system.  You can also 
slice the system up and see what components contribute how much to 
the surface tension, but that is a separate (although related) issue.


At 04:59 PM 12/1/2006, you 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

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-
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry, and of the Center for Biophysics and Computational Biology

Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
3261 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896  Fax 217 244 9757




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Re: [gmx-users] Surface Tension of a lipid bilayer

2006-12-02 Thread David van der Spoel 

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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