Re: correlation functions

From: Thomas Bishop (
Date: Mon Dec 12 2011 - 07:54:06 CST

The tcl interface to VMD has math libraries that can be loaded.
On my system this is done by putting these lines at beginning of my VMD

lappend auto_path /usr/lib64/tcl/tcl8.5 /usr/lib64/tcl /usr/share/tcl
package require Tcl 8
package require math::statistics 0.5
package require math::linearalgebra

Then there's Scipy (phython) which can be run w/in vmd or standalone

and finally if you want it all there's R
and it has a python interface so you can mix and match all the above!


On 12/10/2011 06:03 PM, Boyang Wang wrote:
> This is a long-term issue and must have been under review for a long time.
> On 12/10/11, Aron Broom<> wrote:
>> I had a similar problem once. I didn't find anything in VMD for instance.
>> Grace, the GNU plotting program can do covariance and autocovariance, which
>> is essentially an non-normalized correlation.
>> On Sat, Dec 10, 2011 at 6:18 AM, Molecular Dynamics<
>>> wrote:
>>> Dear Namd users, ******
>>> ** **
>>> I have some NAMD output files for 10 ns with 5000 records. I want to
>>> calculate the correlation functions like -time, -velocity , auto and
>>> cross-correlation functions for analysis. Are there any tools or scripts
>>> for analysis of NAMD outputs to calculate the correlation functions ?****
>>> ** **
>>> Thanks for your help.****

    Thomas C. Bishop
     Tel: 318-257-5209
     Fax: 318-257-3823

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