VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 10 2015 - 16:31:23 CDT

Hi,
  We would also need a copy of the NAMD log file that fails to be able
to debug the code further.

Cheers,
  John

On Wed, Apr 08, 2015 at 06:50:47AM +0000, oguz gurbulak wrote:
> Dear John Stone,
>
> I changed "TOTAL2" in the script with "POTENTIAL" and tried to run it
> again. It computed the average values of TOTAL, TEMP, PRESSAVG and VOLUME
> for my first namd out file. But ıt couldn't work for my second out file.
> I couldn't find where I got the script but I attached "namdstats.tcl" I
> used. Could you please help me to fix the script ?
>
> Regards.
> >Main< (A) 50 % source namdstats.tcl
> Usage: 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, POTENTIAL, TOTAL3, TEMPAVG
> >Main< (A) 51 % data_avg minmd_NPT.out
> Calculating averages...
> CALCULATING DATA FROM TIMESTEP 0 TO 999500:
> BOND: 4108.828256906084
> ANGLE: 2153.6935096991397
> DIHED: 0.0
> IMPRP: 0.0
> ELECT: -116970.09206833366
> VDW: 21827.24498616304
> BOUNDARY: 0.0
> MISC: 0.0
> KINETIC: 2067.3828981303786
> TOTAL: -86812.94240436761
> TEMP: 49.15447203906191
> POTENTIAL: -88880.32530247286
> TOTAL3: -86809.55005141706
> TEMPAVG: 49.14564788415001
> PRESSURE: -487.6260775561439
> GPRESSURE: -368.2150356731323
> VOLUME: 211735.6768608377
> PRESSAVG: -485.595377881658
> GPRESSAVG: -367.8875202654034
>
> >Main< (A) 52 % data_avg md_NPT.out
> Calculating averages...
> can't read "ts(0)": no such variable
> >Main< (A) 53 %
>
> On Monday, April 6, 2015 7:58 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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
> [1]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
> [2]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [3]http://www.ks.uiuc.edu/Research/vmd/
>
>
> References
>
> Visible links
> 1. mailto:vmd_at_ks.uiuc.edu
> 2. http://www.ks.uiuc.edu/~johns/
> 3. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
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/