On 4/22/12 5:39 PM, Andrew DeYoung wrote:
Hi,
I have a system that is effectively two-dimensional. I have two parallel
plates, which are each parallel to the xy plane. Thus, I have what I think
one would call "slab geometry."
Since my system is clearly not isotropic, it does not make sense to compute
radial distribution functions in the standard way (i.e., considering a
sphere around the atom/molecule of interest). Do you know if it is possible
to compute radial distribution functions in cylindrical coordinates?
In the documentation for g_rdf, there is a switch "-[no]xy" which by default
is set to "no." This switch is described as "Use only the x and y
components of the distance." Am I correct in understanding that "-xy" is
effectively computing the RDF in cylindrical coordinates? I guess this
would mean that, for every atom/molecule of interest, you would consider a
cylinder whose axis is parallel to the z axis (and the z axis is
perpendicular to the plates, which are parallel to the xy plane).
When the -xy option is enabled, PBC is turned off in the z-dimension and
distances are computed from the x- and y-components only.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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