VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Sep 18 2009 - 15:36:45 CDT

On Fri, Sep 18, 2009 at 3:53 PM, Goutham <gouthambs_at_gmail.com> wrote:
> Hey All,
>
> Does any of you know of any packages to calculate (velocity)
> auto-correlation? I saw a "signalproc" package here:
>
> http://www.ks.uiuc.edu/Research/vmd/plugins/signalproc/
>
> But this somehow doesn't work. Will be nice if any one can give me pointers
> to it.

hey goutham,

_what_ doesn't work? and _how_ does it not work?
just saying that something doesn't work is not very helpful.
more often than not these problems are a cases of PEBCAC.

the specden command in that package computes spectral
densities directly from convoluted data and can do this with
any data, including velocities. but you don't have the intermediate
VACF but assemble the data directly in fourier space. this is
very adventageous for large data sets and removes the arbitrariness
in traditional VACF based spectraldensities (and avoids the O(N**2)
scaling with correlation length to boot). i have a truckload of those
spectra lying around on my harddrive, and they all look great and
have worked fine. ;)

other than that, programming a VACF directly is embarrassingly
simple in VMD, it just is dog slow.

cheers,
   axel.

>
> Best
> Goutham
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.