Re: namdplot, graph is empty

From: Cetin Baloglu (baloglu_at_gmail.com)
Date: Tue Jun 21 2005 - 15:44:29 CDT

Dear Raeanne,

Namddat script produces a file called data.dat, you should first open
the file if data is in there. If data.dat contains energy values you
want, you have to delete the first header line as xmgrace fails in
strings.
Second if your your locale is UTF-8 or 16, namddat produces a plain
file containing only the headers (awk problem I guess). No data at
all. Previously they offered some solution, it should work, in my case
changing the console language is ok.

In case nothing solves your problem, please attach output of your steps .

Cetin Baloglu

cetinb_at_tezini_yaz:~$ echo $LANG
en_US.UTF-8
cetinb_at_tezini_yaz:~/dynamics/NEW/HEAT$ ./namddat TOTAL 150.out
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC
TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG
GPRESSAVG
Calculating average of TOTAL
cetinb_at_tezini_yaz:~/dynamics/NEW/HEAT$ cat data.dat
TS TOTAL
cetinb_at_tezini_yaz:~/dynamics/NEW/HEAT$ export LANG=en.US
cetinb_at_tezini_yaz:~/dynamics/NEW/HEAT$ ./namddat TOTAL 150.out
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC
TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG
GPRESSAVG
Calculating average of TOTAL
cetinb_at_tezini_yaz:~/dynamics/NEW/HEAT$ tail -2 data.dat
999000 -34460.9782
1000000 -34460.2817

On 21 Jun 2005 14:48:34 -0400, Raeanne Napoleon <raeanne_at_sas.upenn.edu> wrote:
> I am VERY new to NAMD, but not MD. I have tried using both namdplot and
> namddat to get graphs of my ubq_watershpere_equilibration stuff. Each time,
> I get nothing in xmgrace. It seems I have the same problem that a few
> others have in this list, but I tried using their suggestions and they do
> not fix the problem. Please help! Raeanne

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