VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 28 2006 - 14:18:48 CDT

Hi,
  Besides using the external namdplot utilitiy included with NAMD,
you can run the VMD namdplot plugin like this:

package require namdplot
namdplot apoa1.log
namdplot TIMING apoa1.log
namdplot MEMORY apoa1.log
namdplot ELECT VDW apoa1.log
namdplot zero ELECT VDW apoa1.log
namdplot diff TOTAL apoa1.log
namdplot TOTAL vs TEMP apoa1.log

  John

On Thu, Sep 28, 2006 at 02:05:03PM -0500, JC Gumbart wrote:
> Absolutely!
>
> You can find the script here: http://www.ks.uiuc.edu/Research/namd/
> utilities/namdplot
>
> Just save it to a file and then run it. Input is something like: ./
> namdplot ENERGY *.log
>
>
> On Sep 28, 2006, at 12:41 PM, Nicolas SAPAY wrote:
>
> >Hi VMDers!
> >
> >I have a bunch of NAMD outputs to analyze and I want to know if it is
> >possible to use the NAMDplot plugin direclty from the command line
> >in VMD.
> >I just want to load a NAMD ouput file, plot some energies and save the
> >results in xmgrace format
> >
> >Thanks!
> >
> >--
> >[ Nicolas Sapay Ph.D. ]
> >University of Calgary, Dept. of Biological Sciences
> >2500 University Dr. NW, Calgary AB, T2N 1N4, Canada
> >Tel: (403) 220-6869
> >Fax: (403) 289-9311 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078