[CPMD-list] help, draw ELECTROSTATIC POTENTIAL

[Axel Kohlmeyer]

On Sun, 11 Dec 2005, [gb2312] Shangyi Ma wrote:

> Dear CPMD users:

>   Does anyone has the experiences draw the 2D plane contour from the 
> file elpot produced by the keyword ELECTROSTATIC POTENTIAL? I know the

yes.

> file can be display by converting it to the form of elpot.cube and 
> using the VMD software, but I find it's not clearly to see the 
> potential. So I think it's better to draw it in the form of 2D plane 
> contour perpendicular x, y, or z direction and I don't know how to get 
> the datas I needed to finish it. Do I can export the data from the 
> elpot.cube file or from the VMD Volumetric data in other methods? Does 
> anyone has good ideas on the question?

there are several ways to deal with that. the easiest way is probably,
you write a small program that extracts the pice of data that you want
to look at. the cube format is, e.g., described shortly in the first 
part of the file util_p.F from the cpmd sources.

>   Another question is that what's the meaning of "isovalue" when I 
> visualize the Volumetric data in the form of isosurface? I find it 
> shows different shapes in the different isovalue? So how can I get the 
> appropriate isovalue?

an isosurface is a surface, where all points have the same value.
this value is the isovalue. this is most easily understood in atoms
or molecules, if you look at the density. a small (positive) isovalue 
will lead to an isosurface through the low (electron) density area,
and will thus show the 'size' of the molecule.
with the electrostatic potential, this is not that easy, since
you usually have areas of high and low potential which in addition
can be positive or negative.

the appropriate isovalue is the value, that demonstrates, what you
want to show, e.g. if you want to show areas of strong positive and
negativ potentials, you use _two_ representations of different colors
with isovalues of opposite sign. most commonly people 'map' the
electrostatic potential on an isosurface of the 'outside' of a molecule,
so you can see how the molecule is 'seen' from other molecules in terms
of electrostatics, i.e. where the molecule is polarized.

regards,
       axel.

>   Thanks in advance!
>   Best wishes!
>   shyma

=======================================================================
Axel Kohlmeyer    e-mail: akohlmey at cmm.upenn.edu, tel: ++1-215-898-1582
     Center for Molecular Modeling    --    University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.