Re: [ESPResSo] Coloring when using PSF - PDB files ?

[Axel Arnold]

On Wednesday 07 April 2010 04:58:03 Marek Maly wrote:
> Dear all,
> I would like to know how to color particles of different types differently
> in VMD when using PSF/PDB approach.
>
> If I visualise VTF trajectory, VMD automatically uses different colors for
> different particle types as the different particle types are associated
> with
> different atom names in the VTF header which is created with "writevsf"
> function.
>
> On the other hand in case of PDB all the particles/atoms has the same name
> so VMD uses the same color for the whole system. In the last column of PDB
> is particle type but VMD do not care about it, important is just the name
> of atom.

Hi!

if you switch coloring in VMD according to "Segment name" instead of "Atom 
name" in the representation, then the color is chosen according to the T000, 
T001 and so on, i.e. the Espresso type.

Using different atom names is not very helpful, since VMD associates not only 
colors, but also certain sizes with atoms, so that particles of type H are 
smaller than Fe etc, which is most likely not what you want in a coarse-
grained modelling.

Axel

-- 
Dr. Axel Arnold Tel: +49 711 685 63593
ICP, Universität Stuttgart      Email: address@hidden
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70569 Stuttgart, Germany