Dear Jason,
The link is interesting. Thanks for sharing.
Regards
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: Friday, 14 December 2012, 21:24
Subject: Re: [AMBER] extract velocity from traj files
Another option is the script on
http://jswails.wikidot.com/helpful-scripts#toc17 -- it's perhaps more
documented and easier to use.
On Fri, Dec 14, 2012 at 6:46 AM, Vijay Manickam Achari <vjrajamany.yahoo.com
> wrote:
> 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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>
--
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 - 07:00:03 PST
