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