VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Thu May 16 2013 - 09:29:32 CDT

Thanks Mark!! This is very generous of you!
Eddie

On Wed, May 15, 2013 at 10:58 AM, Mark Cunningham <cunningham_at_utpa.edu>wrote:

> Eddie:
>
> Attached is a tcl script that will accomplish what you want. It will work
> with large dcd files
> but it takes a long time to run (single-threaded and interpreted).
> You're best off running it remotely as -dispdev text.
>
> The function draw_corr will also read the output matrix file and connect
> CA carbons (above
> a threshold) that display correlated motion. I found this to be useful.
>
> I used Matlab to plot the resulting correlation images, and have attached
> some .m files that will
> make matrix plots. (The main file is ccplot.m.) Results are illustrated in
> a paper I wrote
> (*J. Mol. Modeling* *18* (2012) 3147-3152)
>
> You'll have to mold this to your specific use but it should give you a
> starting point.
>
> Regards,
>
> Mark
> ------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of
> Prof. Eddie [eackad_at_siue.edu]
> *Sent:* Tuesday, May 14, 2013 11:12 AM
> *To:* vmd-l_at_ks.uiuc.edu
> *Subject:* vmd-l: dynamic cross correlation map
>
> Hi all,
> Has anyone written a Dynamic cross correlation algorithm for vmd? It does
> not seem to have one and I can't find any on the web. I thought I'd ask
> before writing my own.
>
> I'd like a measure of how correlated the motion of one residue is
> compared with every other residue.
> I think what I'm looking specifically is a function that could (for each
> frame or average over all time frames) calculate C_ij =
> <r_i*r_j>/sqrt[<r_i^2><r_i^2> ].
>
>
> Thanks,
> Eddie
>
> --
> _________________________________________________________
> Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
> Assistant Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390
> 

-- 
_________________________________________________________
Edward Ackad, Ph.D <http://www.siue.edu/%7Eeackad>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390