Re: Yan: analysis question

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Fri Jul 22 2011 - 03:01:05 CDT

On Thursday 21 July 2011 15:10:26 Namd Namd wrote:
> Dear Bjoern,
>
>
> Thank you very much for your reply. I examined your site and found it very
> useful.
>
You are welcome.
But please always CC the Mailing-list for further questions. Others might
benefit from your question and/or my answer.

> Thanks for your valuable effort. I want to use your script anamo.py for
> writing pressure tensor elements.
>
You are talking about PXX PXY PXZ PYX PYY PYZ PZX PZY PZZ, aren't you?

> But, I have not enough information about python programming language.
>
You don't need to know anything about Python to run the script.

> How can I regulate your script to write pressure tensor elements for a
> “namd.log” file ?
>
You don't have to regulate anything, just run it with the according parameters
something like:

# python anamo.py --help

or in your particular case, to plot and extract PXX and PXY at the same time:
# python anamo.py -x PTS -y PXX -x PTS -y PXY -o out -f namd.out

This will produce six files:
PTS-PXX_out.dat
PTS-PXX_out.dat.{svg,png}
PTS-PXY_out.dat
PTS-PXY_out.dat.{svg,png}

The dat files will contain the raw data you see in the plot.

And anamo will print out MIN, MAX, STD for every selection to std-out.

All you need is python >=2.5, scipy and matplotlib.

http://python.org/
http://www.scipy.org/
http://matplotlib.sourceforge.net/

On windows you might consider the Enthought Python distribution, since it
contains the above modules.
http://www.enthought.com/products/edudownload.php (scroll down to academic)

Or use (I would prefer this)
http://www.activestate.com/activepython/downloads
and install the required modules one by one with PyPM (comes with activpython)

If this is to much hassle, use VMDs "NAMD Plot" to extract the data.

> Which changes should I make in script ? Could you please help me about this
> issue ?
>
Don't change anything except you know what you are doing or you have to squish
some bugs ;-)

Cheers,
Bjoern

> ________________________________
> Kimden: Bjoern Olausson <namdlist_at_googlemail.com>
> Kime: Namd Namd <namd_10_at_yahoo.com>
> Kopya: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
> Gönderildiği Tarih: 19 Temmuz 2011 13:43 Salı
> Konu: Re: namd-l: analysis question
>
> On Tuesday 19 July 2011 11:32:06 Namd Namd wrote:
> > Dear Namd experts,
> >
> >
> >
> > How can I write the Px Py Pz pressure tensor elements and
> > forces acting on each atom to an output file ( like pdb or .coord and
> > .vel ascıı format ) for analysis ?
>
> If you are referring to the information contained in the NAMD output file,
> you can use VMD "NAMD Plot" plug-in or write a tool on your own which
> grabs the desired information from the NAMD output file like I did:
> http://olausson.de/scriptarchive/16-modeling/56-anamopy
> There are a lot of little helpfull tools out there, just use Google to find
> them.
>
> > And Can acceleration information for each
> > atom be written as an output ?
>
> Please read the UG and search the mailinglist:
> http://www.ks.uiuc.edu/Research/namd/2.8/ug/node13.html#SECTION000622000000
> 00000000 http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4125.html
>
> Kind regards,
> Bjoern

-- 
Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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