VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Jul 03 2009 - 11:04:53 CDT

On Wed, 2009-07-01 at 14:19 +0200, Bjoern Olausson wrote:

> > > PRESSURE: 29109200 546.983 413.11 92.8291 413.11 -486.118 30.045 92.8291
> > > 30.045 -566.529
> > > GPRESSURE: 29109200 388.5 383.831 6.4171 339.175 -407.812 358.594
> > > -111.003 -223.426 -491.163
> > > PRESSAVG: 29109200 32.2755 -27.1969 -120.07 -27.1969 8.01839 -60.9932
> > > -120.07 -60.9932 -3.92224
> > > GPRESSAVG: 29109200 30.6858 -30.7705 -117.957 -14.7335 12.1397 -64.4612
> > > -123.885 -49.5245 -4.49357
> > > ENERGY: 29109200 2828.8126 8444.6120 4596.9095
> > > 59.0735 -39328.9221 -1866.4500 0.0000 0.0000
> > > 13455.6967 -11810.2678
> >
> > sorry, this doesn't make any sense to me. you seem to be quoting part
> > of a NAMD output file, but that has _nothing_ to do with the protein
> > database atomic file format.
> >
> You are right, that does not have anything to do with PDB format, it was just
> an example for a good documented file format ;-) Is there a similar
> description for the NAMD output file? (Is it whitespace separated, fixed
> columns...)

it is quite a stretch to compare a file format that is meant for
data exchange with the status output of an MD code. the canonical
answer to the format is - of course - to ask you to look it up
in the NAMD source code or in the namdplot plugin script.

[...]

> > if you want to plot the data from a simulation run, have a look at
> > the namd plot plugin already bundled with VMD. no need to re-invent
> > that wheel again. ;)
> > http://www.ks.uiuc.edu/Research/vmd/plugins/namdplot/
> >
> I know about this plugin, but it is to inflexible for my purpose and I wrote
> one for CHARMM which is easily adopted to NAMD output ;-) And it is way more
> comfortable to just launch 'anamo.py -f "*.out" -x Time -y TEMPAVG' and get a

have you checked out the command line interface of namdplot?

but of course, everybody writes code the way he or she prefers
it, and everybody has different preferences. i understand why
you want to stick to your scheme.

cheers,
   axel.

[...] 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.