Re: Formating of logfile

From: Axel Kohlmeyer (
Date: Sat Nov 14 2009 - 10:11:01 CST

On Fri, Nov 13, 2009 at 10:47 PM, Bjoern Olausson
<> wrote:
>> bjoern,
>> i have a stupid question: what is wrong with the "NAMD Plot"
>> plugin in VMD?
> I guess nothing... I just love python and when I write my own program,
> I am more flexible. Second, I don't like TCL/TK very much ;-)

fair enough. i'll take the liberty to ignore the flame bait. ;-)

> This code resulted out of the fact that I had to plot some results
> from CHARMM (as far as I know there is no tool to plot the CHARMM
> output). Then, moving the simulation from CHARMM to NAMD I just ported

there probably is, too. people have been using CHARMM for so long,
there _have_ to be all kind of tools. ;)

> the script cause I was used to it. I still do many analysis with
> CHARMM (I might do them as well with VMD, but I am not that into
> TCL/TK so I am faster of with CHARMM and/or Python).

well, not having to write a script at all is in general even faster.
hence my question.

>>why invent another new wheel?
> To sum it up: I just might be to lazy looking deeper into TCL/TK which
> implies the fact, that I am more flexible and faster with my little
> script and I want to improve my python skills (there's still a lot to
> improve!)
> Satisfied?

it satisfies my curiosity. thanks. if i may make a suggestion: if you want
to improve your python skills, why not try and write some python based
plugins to be included into VMD?

there seem to be a lot of people around that emphatically love python
and ask for better python support in VMD (internally and scripts/plugins),
but somehow it always seems to stop at the point of writing something
more general.

> But now let me ask a stupid question:
> Now that I explained myself, why not simply answer my question? ;-)

because it is so simple to find out for yourself! the output is simple
c++ style white space separated columnwise output with the column
assignment in a header line. see the namd source (Controller.C) for details.

> Bjoern.

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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