Electrostatic Potential in Gaussian94 Cube format generated with NWCHEM

Short Url to this page http://goo.gl/FKZXj

(3/20/14) Last release of Nwchem include Gaussian(TM) cubes already in Properties module

SEE : http://www.nwchem-sw.org/index.php/Release64:Properties#Gaussian_Cube_Files

The propose of this patch is provide to NWCHEM users the capability to generate an electrostatic potential

cube to be graphical represented by popular molecular visualizers, ie. gOpenmol, Molekel, Molden, VMD.

Instructions

In order to add this feature, you have to download the SVN version of NWChem of Oct-2011, here.

Also to download the patch file from the attachments at the end of this page and to copy it to the your

$NWCHEM_TOP/src. Then, to execute the command patch:

patch -p0 < patch.esp-gcube.jgo-nwchem-6.0

Finally compile the NWChem ensuring that the module 'esp' is included in the modules of your environmental

variable $NWCHEM_MODULES.

Example

The subroutine code can activated with the presence of 'esp:fullesp 1' in the runtime database.

Water molecule

Here we show an example input to generate the electrostatic potential (ESP) cube of the water molecule

intermediately after a single point of energy calculation using the method HF/cc-pVTZ, would like as follow:

title "water esp hf/cc-pvtz"

start h2o

geometry autosym

O 0.0 0.0 -0.02

H -0.74 0.0 -0.76

H 0.74 0.0 -0.76

end

basis

* library cc-pvdz

end

scf

print low

end

task scf

set esp:fullesp integer 1

esp

range 0.3

spacing 0.01

end

task esp

Once this calculation finishes successfully, you would find a file with the extension h2o.grid, this file will contain the ESP in the g94 format.

Visualization examples

Contour colorized plot generated by gOpenmol** of the Electrostatic Potential on the range of -.09 (blue velvet) and .09 (read), the 0.0 is represented by green color.

Plot generated with Molekel***of the isosurfaces of the Electrostatic Potential with cutoffs of -.07 (on red) and .07 (blue).

Acknowledgment

This piece of code is based on a modified version of NWChem created by Dr. Jorge Garza from the Universidad Autónoma Metropolitana.

References

Gaussian Cube Files , Prof. Paul Bourke

http://paulbourke.net/dataformats/cube/

cubegen Gaussian INC,

http://www.gaussian.com/g_tech/g_ur/u_cubegen.htm

** gOpenmol

http://www.csc.fi/english/pages/g0penMol

*** Molekel

http://molekel.cscs.ch//wiki/pmwiki.php