VMD-L Mailing List

From: Wang Xianqiao (xqwang1022_at_gmail.com)
Date: Sat Oct 30 2010 - 19:02:25 CDT

Dear Axel,

I try to say: in what format I can plug in more information about atoms
(besides the XYZ trajectories) such as displacements, charges, temperature.
So I can plot contour figure according to those quantities in VMD. My ideal
format is

frame1
number atom type x y z displacement charges
temperature stress1 stress2 stress3
       1 C 0.1 0.1 0 0 0
              300 0 0 0
       2 C 0.1 0.2 0 0 0
              300 0 0 0
      ......

frame2
number atom type x y z displacement charges
temperature stress1 stress2 stress3
       1 C 0.1 0.15 0 0.5
  0 300 0.1 0 0
       2 C 0.1 0.25 0 0.2
  0 300 0.2 0 0
      ......

According to the quantities ( except x y z), I can plot the contour figure
for different frame.
Is it possible?

Best,

Xianqiao

On Sat, Oct 30, 2010 at 11:56 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Sat, Oct 30, 2010 at 12:47 AM, Wang Xianqiao <xqwang1022_at_gmail.com>
> wrote:
> > Dear all VMDs,
> > I try to plot contour figures of atoms. Contour figures may be
> trajectories,
> > or other field quantities of atoms (I can get outside the input file).
>
> i don't understand what you are asking for.
> can you give some example of how this should
> look like and how this would be computed?
>
> > Or if there is a way to allow one to use different name to represent the
> > same atom in different frame in XYZ format. For example, I have 10 atoms
> > first frame have the same name C, but in the second frame, I want to
> change
> > the first five as D according to some quantities. But I can not show
> > different color in the second frame. Many thanks,
>
> yes. this is not a bug, this is a feature. it has been discussed on this
> list _many_ times before. make sure you check the archives. VMD has
> been optimized for classical bio simulations and there atom identities
> don't change. you have to keep in mind, that the .xyz file format is about
> the worst possible format, since it is the lowest common denominator.
>
> you can store time varying per atom properties in the user, user2, user3,
> user4 fields and then use that to color or select atoms. there are other,
> more elaborate schemes possible, by tracing the frame counter for your
> molecules. those require some knowledge of Tcl (or Python). some Tcl
> examples are presented in this pdf
>
> http://sites.google.com/site/akohlmey/redirect/cpmd-vmd.pdf?attredirects=0&d=1
>
> cheers,
> axel.
>
> > Best,
> > Xianqiao Wang
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>