VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Thu Apr 28 2005 - 01:12:24 CDT

On Wed, 27 Apr 2005, Michel Espinoza-Fonseca wrote:

hi guys,

if i understood yongcheng's mail right, this is about the visualization
and not the calculation.

to visualize the electrostatic potential mapped onto a molecular
surface, you need the latest version of VMD (currently 1.8.3) and
then create your molecular surface visualization and load the
data of the electrostatic potential into the same molecule as
volumetric dataset (depending on how you calculate it the format
is different, but VMD supports quite a few formats), choose
the coloring method 'Volume' and then select the data set.
in the Trajectory tab you can set the range of the color scale,
which you usually should adapt to be symmetric around zero,
so the colorization is most helpful.

if you use data generated from quantum chemical calculations, you
may want to have a look at
http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part5.html#chap7_sect1
which demonstrates (amongst others) that process for data in the
.cube file format.

beware, your graphic card driver needs to support OpenGL textures
correctly for that and with PC hardware this can be tricky.

best regards,
        axel.

> Are you obtaining the PES and then visualize it using VMD? If your
> answer is "yes", the you can calculate the PES using the program APBS
>
> http://agave.wustl.edu/apbs/
>
> Nathan Baker wrote a nice tcl script to visualize the PES using vmd. You
> can find more information about the script here:
>
> http://agave.wustl.edu/apbs/doc/html/tutorial/index.html
>
> You can also load files from GRASP, to visualize the PES.
>
> Hope it helps
>
> Peace,
> Michel
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf
> Of Yongcheng Zhou
> Sent: Wednesday, April 27, 2005 5:12 PM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: color the surface with electrostatic potential value
>
>
> Dear all,
>
> I was keeping read figures from journal papers which says that the
> molecular surface was colored with the electrostatic potential values.
> I do know that we can plot the isosurface of the potential field however
> I really don't have any idea to color the molecular surface with
> the potential value, in other words, to project the potential onto
> the molecular surface.
>
> Hope the problem is well posed and any hint is really appreciated.
>
> -yc
>
> MSU
>
>
>
> 

-- 
=======================================================================
Dr. Axel Kohlmeyer   e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.