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From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Feb 19 2008 - 18:54:53 CST

Oops, forgot to attach the image.

---------- Forwarded message ----------
From: L. Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu>
Date: Feb 19, 2008 6:52 PM
Subject: spacial distribution function
To: vmd <vmd-l_at_ks.uiuc.edu>

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


rlc-hc-3-129-gr.png