VMD-L Mailing List

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Mon Jul 06 2009 - 07:10:37 CDT

On Friday 03 July 2009 18:04:53 Axel Kohlmeyer wrote:
> On Wed, 2009-07-01 at 14:19 +0200, Bjoern Olausson wrote:
> >
> > 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.
>
I finally figured it out :-)
PRESSURE, GPRESSURE, PRESSAVG,GPRESSAVG are white space separated

ENERGY is fixed column:
0:7 16:31 31:46 46:61 61:76 76:96 96:112 112:126 126:141 141:156 156:176
176:191 191:206 206:221 221:236 236:256 256:271 271:286 286:301 301:316

> [...]
>
> > > 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?
>
nope I didn't wasn't aware of the command line interface of namdplot. Looks
promising and looks like it makes my script more or less obsolete.

Thanks for your help!

kind regards
Bjoern