Dear Jason,
Well, I could trace out the problem I faced. In my traj file, there are 200 frames. The python code read the first frame as "0" and the last frame as "199" which is equivalent to 200th frame.
Other wise the script works fine.
Thank you.
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
________________________________
From: Vijay Manickam Achari <vjrajamany.yahoo.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Friday, 14 December 2012, 13:03
Subject: Re: [AMBER] extract velocity from traj files
Thanks for the reply.
By the way, I have tried reinstall python-scientific. Then tried to run the script nctorst.py. In the script I changed " frame = 200" and "inputfile = 'waters1445-MD010-run1000.traj' " . Because each traj file contains 200 frames.
When I run the script typing python nctorst.py, I get error message as below
vijay.glycosim:~/Simulation-Folder-oct2012/water-only/Production-waters1445$ python nctorst.py
title 200
Traceback (most recent call last):
File "nctorst.py", line 31, in <module>
print "%5i%15.7e" % (shape[1],ncfile.variables['time'][frame])
IOError: Index exceeds dimension bound
vijay.glycosim:~/Simulation-Folder-oct2012/water-only/Production-waters1445$
I am little bit lost here. Is this script need any other input?
Appreciate any help.
Regards
Vijay
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: Vijay Manickam Achari <vjrajamany.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Thursday, 13 December 2012, 20:54
Subject: Re: [AMBER] extract velocity from traj files
On Thu, Dec 13, 2012 at 4:08 AM, Vijay Manickam Achari <vjrajamany.yahoo.com
> wrote:
> I would like to extract velocity from trajectory files.
> I have used ntwv = -1 and ioutfm = 1 in the input parameter file.
>
> According to AMBER mailing list (
> http://archive.ambermd.org/201011/0255.html), I installed
> python-scientific in Ubuntu-11.10
> and tried to execute the script. But It failed to run.
>
> The output is as below:
>
> [vijay.glycogpu extract-vel]$ python extractvel.py
> Traceback (most recent call last):
> File "extractvel.py", line 1, in <module>
> from Scientific.IO.NetCDF import NetCDFFile as Dataset
> ImportError: No module named Scientific.IO.NetCDF
> [vijay.glycogpu extract-vel]$
>
>
> Is there anything additional things need to be done?
> Please advice.
>
On my Ubuntu system (12.04), after installing python-scientific,
Scientific.IO.NetCDF.NetCDFFile could be imported without any problems (and
the likelihood that 11.10 is broken in this regard is very low). My guess
is one of two things happened: you have another (non-system) python (type
'which python' to make sure that it returns /usr/bin/python) that is being
invoked by default -- this 'other' python would not have the Scientific
package. Or, python-scientific did not install properly. Note the
difference between scipy and ScientificPython -- they are distinct packages
that do different things.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Dec 14 2012 - 04:00:01 PST
