VMD-L Mailing List

From: oguz gurbulak (gurbulakoguz_at_REMOVE_yahoo.com)
Date: Wed Apr 08 2015 - 01:50:47 CDT

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------=_Part_2109291_488477645.1428475848064--
------=_Part_2109292_229610760.1428475848068--