VMD-L Mailing List

From: Goutham (gouthambs_at_gmail.com)
Date: Fri Sep 18 2009 - 22:25:02 CDT

> >...and again "it doesn't work" doesn't help at all!!
>

package require signalproc

gives an error message:
can't find package signalproc

However :
package require specden

loads fine without any error.

Also the IRspec GUI works fine!
-----

> doesn't work how? is there an error message? if yes, which one?
> which version of VMD do you have? which platform?
>
>

I have tried VMD1.8.4, VMD1.8.6 on linux. The above mentioned specden
package loads up on my Mac running VMD1.8.6.

i am confused! how can it make your life easy, if it doesn't work for you???
>
>

When I tried using the IRspecGUI on the linux machine, it worked fine. I
computed spectral density from the veldcd, and the peaks were as I expected.
Which is the part that works. The script doesn't work though.

However teh actual case for which I want to compute the spectrum, is very
big in size (8GB), and my computer freezes when I load the dcd file. I am
thinking if I tried a script version, I probably won't have that issue.

Thanks
Goutham

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