Re: Yan: analysis question

From: Bjoern Olausson (
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 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 --help

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

This will produce six files:

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.

On windows you might consider the Enthought Python distribution, since it
contains the above modules. (scroll down to academic)

Or use (I would prefer this)
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 ;-)


> ________________________________
> Kimden: Bjoern Olausson <>
> Kime: Namd Namd <>
> Kopya: "" <>
> 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:
> 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:
> 00000000
> 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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