VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Feb 19 2008 - 19:48:02 CST

Ok, after taking a short break (my head seemed to be full other
things), I think that the best solution will be to fit those distances
to a new distribution of probabilities (instead of g(r), which doesn't
make sense for my very specific purposes). That does the work. In any
case, all comments are still welcome.

Cheers,
Michel

On Feb 19, 2008 6:52 PM, L. Michel Espinoza-Fonseca
<mef_at_ddt.biochem.umn.edu> wrote:
> 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
>