From: Thomas Bishop (bishop_at_latech.edu)
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
scripts
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
http://www.scipy.org/
and finally if you want it all there's R
http://www.r-project.org/
and it has a python interface so you can mix and match all the above!
Cheers,
Tom
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<broomsday_at_gmail.com> 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<
>> moleculardynamics_at_yahoo.com> 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
http://dna.engr.latech.edu
********************************
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