VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 06 2015 - 10:17:46 CDT

Hi,
  You didn't say where you obtained your "namdstats.tcl" script from, so
it is hard to guess what might be wrong with the version you have.
Google shows that there are several versions of this script floating around.
You may have an old one that has not been corrected for the most recent
vesions of NAMD. The current versions of NAMD no longer emit a field
named "TOTAL2", it now emits "POTENTIAL" instead. This breaks scripts
that are expect to read "TOTAL2" and don't have any fallback code if it's
not there. I assume that your namdstats.tcl script tries to read TOTAL2,
so you may want to try and replace "TOTAL2" in the script with "POTENTIAL"
and see if it cures your problem or not. If not, then you'll need tell us
where you got the script and/or who wrote it and we'll help them get it fixed.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Apr 05, 2015 at 09:54:50PM +0000, oguz gurbulak wrote:
> DearAll,
>
>  
>
> Iwanted to compute the average values of TOTAL, TEMP, PRESSAVG and VOLUME withusing ???namdstats.tcl??? script for a NPT run. But I got theerror ???can't read "ts(0)": no such variable???.How can I solve this problem ? Could you please help me about this issue ?
>
>  
>
> Regards.
>
>
>  >Main< (A) % source namdstats.tclUsage: data_avg <logfile>[<first timestep> <last timestep>]
>
>    <first timestep> and<last timestep> may be entered as numbers or
>
>    <first timestep> ='first' will start at the beginning of the simulation
>
>    <last timestep> ='last' will go to the end of the simulation
>
> Usage: data_time <data stream><logfile> [<first timestep> <last timestep>]
>
>    <data stream> = BOND,ANGLE, DIHED, IMPRP, ELECT, VDW, BOUNDARY, MISC, KINETIC, TOTAL, TEMP, TOTAL2,TOTAL3, TEMPAVG
>
> >Main< (A)  % data_avg namd_1.out Calculating averages...
>
> can't read "ts(0)": no suchvariable
>
> >Main< (A)  %
>
> 

-- 
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/