Re: Formating of logfile

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Sat Nov 14 2009 - 20:42:37 CST

On Sat, Nov 14, 2009 at 17:11, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Fri, Nov 13, 2009 at 10:47 PM, Bjoern Olausson
> <namdlist_at_googlemail.com> 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. ;-)
>
What a pity! Would have brought some fun to the mailinglist members :-)

>> 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.
>
That's indeed true.

>>>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.
>
I guess it's the fact that one would have to deal with the API of VMD
and that implies spending some additional time.
I wouldn't consider my python skills good enough to contribute to the
enhancement of VMD/python integration.
But anyway, I'll take a look the VMD/python approach at some time and
play a bit around when I find some time.
Anything you can point me to?

>> 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.
>
Mmmh, you might not know, but I am a biochemist, I actually never
learned coding explicitly and and looking at C code, thought I can
read and understand it up to some point, scares me away every time :-)

> axel.
>
Cheers
Bjoern

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:51:41 CST