VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Mon Feb 09 2015 - 10:36:55 CST

Whether you are calculating a local or global cross correlation depends on
how you call the function. Calling the correlation function without the
-threshold option set will calculate a global correlation. If you want a
local correlation, you need to set the -threshold (measured in sigmas), to
effectively cut off the density further out from the structure. Secondly,
by the other definition of local, you can choose which part of structure
you are using to calculate the correlation by the atom selection passed to
the function.

On Mon Feb 09 2015 at 7:13:45 AM Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk>
wrote:

> Dear Users,
>
> I am currently using the MDFF package in VMD to calculate the
> cross-correlation coefficient of my MDFF trajectories. I am curious that
> whether it is calculating a global CCC or a local one.
>
> Thanks in advance,
>
> Kevin
>
> PhD Candidate
> Department of Physics and Materials Science
> City University of Hong Kong
>