Re: [ESPResSo-users] PDB files

[Christoph Junghans]

2015-11-09 8:32 GMT-07:00 Paul Peterson <address@hidden>:
> 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.
Yep, it is a secret option!

>
> 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
>
>



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