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Re: [ESPResSo-users] PDB files

From: Paul Peterson
Subject: Re: [ESPResSo-users] PDB files
Date: Mon, 9 Nov 2015 16:32:03 +0100

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.



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: <>
writepdb has an option "-names" to hand over a list, which serves as a
map of the Espresso ids to names.


> Thanks,
> Paul

Christoph Junghans

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