Re: [ESPResSo-users] PDB files

[Paul Peterson]

Thanks Peter - I've switched to vtf files and it's getting better now.

Thanks, Cristoph, for mentioning that option -names which I really can't find in the manual.

Best,

Paul

2015-11-09 16:15 GMT+01:00 Christoph Junghans <address@hidden>:

2015-11-09 6:27 GMT-07:00 Paul Peterson <address@hidden>:
> Hi,
>
> I'm quite new to ESPResSo and MD simulations in general, so mine could be a
> very naive question.
>
> I have two types of particles and in my simulations.
> In output files produced by writepdb, all my particles are (arbitrarily)
> labeled "Fe", although the type distinction is preserved (last column).
> That's the reaon, I suppose, why Jmol will display them all the same, nor do
> I find a way to colour them according to the type.
>
> I looked for options in the writepdb command, but couldn't find any in the
> Manual.
> Any suggestions (also about more conveniente file formats)?
See: <https://github.com/espressomd/espresso/blob/master/scripts/pdb.tcl#L128>
writepdb has an option "-names" to hand over a list, which serves as a
map of the Espresso ids to names.

Christoph


>
> Thanks,
>
> Paul



--
Christoph Junghans
Web: http://www.compphys.de