[gmx-users] Pressure coupling type for Biomembrane simulation

[Eric Jakobsson]

I think there is no reason for having cross-terms (xy/yx, etc.)

For bilayers, there is a string of published papers about whether the 
surface tension should be zero or non-zero (i.e., should the pressure in 
the normal direction be different from that in the membrane 
plane.).  And--if it is non-zero, how large should it be?  I think the 
issue is not resolved, but using 1 atmosphere all the way around will be at 
least sort of o.k., and nobody will get mad at you---for bilayers.  For 
monolayers, the surface tension is clearly non-zero, as one can measure it 
in the Langmuir trough experiments, so in monolayer simulations the 
pressure in the membrane plane should be non-zero, and in fact should be 
negative.

At 06:55 PM 12/30/2003 -0600, you wrote:
>Dear Gromacs mailing list:
>
>I am doing the biomembrane simulaiton, I am wondering that now the experts
>in the Biomembrane simulations deal with the pressure coupling type for
>Biomembrane simulation. Using pcoupltype as isotropic or anisotropic, which
>one is more physiological reasonable? Also if choosing the anisotropic, what
>should be the 6 pressure scaling values needed for xx, yy, zz, xy/yx, xz/zx
>and yz/zy components respectively.
>
>Thank you very much in advance.
>
>Thanks,
>
>Yuhua
>
>
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---------------------------------
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909
(Currently on leave to the National Institutes of Health in Bethesda, 
Maryland, to be Director of the NIGMS Center for Bioinformatics and 
Computational Biology and Chair of the NIH Biomedical Information Science 
and Technology Initiative Consortium, but maintaining my research lab at 
Illinois by periodic commuting.  My usual schedule is four days a week at 
NIH and three days a week at Illinois.)