VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Oct 30 2010 - 19:17:46 CDT

On Sat, Oct 30, 2010 at 8:02 PM, Wang Xianqiao <xqwang1022_at_gmail.com> wrote:
> 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

sorry, i still don't understand what you mean by "contour figure".
the only context where i know "contour graphs" are software that
operates on gridded data. but VMD is not that kind of software.

> 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?

as i alluded to previously, you cannot read in arbitrary data
through the molecule file reader plugins, at least not yet.
in any case you would have to write your own plugin, if you
want to read a custom file format.

currently you essentially have to use the "user" type fields
for storing that kind of data. that will have to be done with Tcl
(or python scripting) and the pdf i pointed you to, gives a
few examples for Tcl.

axel.

> Best,
> Xianqiao 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.