VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jul 14 2015 - 11:45:56 CDT

On Tue, Jul 14, 2015 at 11:20 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
> Hi,
> If Axel isn't able to answer your questions (he wrote signalproc),
> your best bet would be to read the signalproc code and determine
> if you can easily modify it to suit your needs yourself.

sorry for the late reaction. i had seen the post, but then got
distracted and then forgot about it.

some comments on this.

- i don't think the component spectra are actually additive in
general. if at all, then you'd have to use the unreweighted spectrum
(option "fourier").

- the choice of enforcing the normalization was done for two reasons:
1) to simplify comparing spectra produced from different input data
and with different resolution. 2) since we have no access to
transition moments, the absolute intensities are pretty meaningless
anyway.

- a straightforward approach would be to add an option (lets call it
"none") to it select outputting the unnormalized, unreweighted
spectrum.

this is easily done from source. i can probably produce updated plugin
binaries quickly for some selected platforms.

ana, what platform are you running on?

axel.

>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Jul 09, 2015 at 05:34:08PM +0200, Ana Celia Vila Verde wrote:
>> Hi everyone,
>>
>> I've used the signalproc package to calculate the power spectrum
>> within the harmonic approximation. The calculated power spectrum is
>> normalized so that the sum of all y-values equals unity (as
>> indicated in the signalproc webpage; I also checked this myself). My
>> question is: is there a way of disabling this normalization? I
>> would like to do it because I'd like to know how much each component
>> of the system contributes to the total spectrum. I've calculated
>> the power spectra of individual components of my system but because
>> of this normalization factor, I cannot assess their relative
>> intensity.
>>
>> Thanks,
>>
>> Ana
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.