[gmx-users] Radial distribution function (RDF) in cylindrical coordinates

Justin A. Lemkul jalemkul at vt.edu
Sun Apr 22 23:48:41 CEST 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list