From: Erik Nordgren (nordgren_at_sas.upenn.edu)
Date: Thu Sep 09 2004 - 13:56:27 CDT
Hi everyone,
My first post on this subject was cheerfully ignored :) so I'll try again,
maybe with fewer words to hold the attention better!
Basically, I want to understand how the "surface tension" algorithm does its
thing in NAMD. When using Langevin constant-pressure, there is an option to
set a value for the "SurfaceTensionTarget", but all the User Guide says is:
"The pressure specified in LangevinPistonTarget becomes the pressure
along the z axis, and surface tension is applied in the x-y plane."
The thing is, I'm confused by how this might be implemented. Is it just an
addition to the X and Y components of the isotropic pressure tensor? If so,
how is surface tension (in force/length) translated to pressure (in
force/area)? Does it normalize according to the height (Z dimension) of the
MD box?
Furthermore, "surface tension" (and "surface pressure" too, for that matter)
are only physically defined for a *surface* (i.e., an interface between two
bulk materials, like octane/water). But surely NAMD doesn't "know" if there
is a surface present in your simulated system. On the other hand, even if
your system is just a box of water, you can still tell NAMD to hold its
"surface tension" to some value. So, what is the program really doing?
More concretely: if the real-world system I am trying to model is, for
example, a phospholipid monolayer on water, held at a surface pressure of 20
dyn/cm, do I simply use that value for "SurfaceTensionTarget" in NAMD and
all will be well?
For those who would like to read more, here is my first post on the issue:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1261.html
Anyone who can shed some light, I'd be grateful!
- Erik
C. Erik Nordgren, Ph.D.
Department of Chemistry
University of Pennsylvania
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