VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 25 2019 - 10:34:27 CDT

Hi,
  There are various programs that can compute cross correlations
between a density map and an atomic structure. The code for
calculating MDFF cross correlations in VMD is much much faster
than any of the other tools that I'm currently aware of, so
I would of course strongly recommend that you use VMD to do it.

You can run VMD in batch mode (e.g. text commands), and even in
parallel on clusters or supercomputers to do these calculations on a
large scale for large structures, big trajectories, or in cases where
you wish to calculate a large number of cross correlations for
individual components of your structure.

It's not clear what you're asking when you say "without opening the VMD"?

We describe how one can run large batch mode parallel CC calculations
in the 2014 Faraday Discussions paper where we published our
fast MDFF CC algorithms:
  http://dx.doi.org/10.1039/C4FD00005F
  https://pubs.rsc.org/en/content/articlelanding/2014/FD/C4FD00005F#!divAbstract

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 25, 2019 at 05:26:41PM +0200, Mihaljevic-Juric Paula (Mme) wrote:
> Hi,
> I have rather large system and I am dealing with large set of data. I
> would like to do analysis of cc, but without opening the VMD.
> I was wondering how is it usually done and if there is any example for it
> online?
> Or perhaps it would be easier to calculate it without a plugin or another
> tool?
> Thank you
> Paula 

-- 
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/