VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Sep 18 2009 - 16:18:44 CDT

On Fri, Sep 18, 2009 at 4:52 PM, Goutham <gouthambs_at_gmail.com> wrote:
> 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.

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

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

what did you try? what did you expect? and what did you get instead?

unless you provide sufficient data to reproduce it, nobody will be
able to debug it. it works just fine for me, but then again. i don't
usually use the precompiled binaries, but the bleeding-edge cvs
code with lots of local modifications, so i don't know much about
the downloadable packages and especially about platforms like
MacOS or Windows that i don't use at all.

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

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

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.