VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Feb 19 2008 - 18:52:15 CST

Hi all,

I'm trying to obtain distribution function of two residues (or Ca
atoms) from a MD simulation. I was playing around with the Radial Pair
Distribution function plugin included in VMD and it seems to do a good
job for the type of analysis I need. I was using the plugin without
the PBC option (so image-image pairs are not included), but the output
(as already mentioned in the help webpage) are quite odd. So I was
wondering if there is already a plugin to calculate the spacial
distribution function or if there is a way to somehow get meaningful
numbers.

Attached please find a graph of what I'm obtaining. Basically, in
terms of probability, I should be getting a larger peak at r ~ 55 A
(please see attached image); instead I get a very short peak, which of
course doesn't make sense. I have to point out that I'm analyzing 2
different MD simulations, but the length of simulation is the same.

All comments will be highly appreciated.

Cheers,
Michel