VMD-L Mailing List

From: Goutham (gouthambs_at_gmail.com)
Date: Fri Sep 18 2009 - 15:52:44 CDT

Hey Axel,
  I should have said more that just say "does not work". I sent the email,
and then realized it myself that I didn't say enough. I am sorry about that.

Well, I discovered the IR Spectral Density plugin in VMD, which works for
me. However I was trying a script version, and tried to load :

package require signalproc

and this doesn't work. Perhaps I am missing something.

Any help would be appreciated. BTW, thanks for writing this package into
VMD. Makes my life easy. :-)

Best
Goutham

On Fri, Sep 18, 2009 at 1:36 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>