Lee Soin wrote:
This seems to me a very complicated realization. Why doesn't
GROMACS provide an easy way for wall simulation?
How about reading manual section 7.3.20 "Walls" in the Gromacs-4.0 manual? I
think that would be what you're after.
-Justin
2008/10/11 Omer Markovitch <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
Oh, I didn't read carefully.
My suggestion would be, perhaps, to physically put atoms on the
sides of the box (possibly, fill each side completely), and to place
on them very high repulsion.
You might want to freeze them up, and exclude their self
interactions from the energy calculation.
Good guess Suman. Omer.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
On Sat, Oct 11, 2008 at 09:26, Suman Chakrabarty
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote:
Possibly what he is interested in is a system WITHOUT PBC? I
don't think
with PBC the system is really "confined", since there is no true
wall to
reflect the colliding molecules. Thus to study the effect of real
confinement, it is necessary to remove PBC and impose reflective
boundary conditions. I am only guessing! :)
--Suman.
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Virginia Tech
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