Wednesday, July 24, 2013

A python program for reading coordinates and gradients from a GAMESS output file

Some people liked the previous post on python, so I dusted off this python program for reading locating coordinates and gradients in a GAMESS log file and writing out and .xyz+vib file (to create this post).  I have only used it on this output file, but it should work for other files as well.

Even if you have no interest in .xyz+vib files, the program might be useful as an example of how to locate specific information in a file and read it in. If you have similar programs (or questions) please feel free to share them in the comments

Tuesday, July 23, 2013

Illustrating energy minimization: a simple python program

Here is a simple python program I wrote to illustrate energy minimization.  The program uses steepest descent and a force field to minimize the energy of a water molecule in internal coordinates.

If you have a Mac or Linux machine you already have python installed (Windows users please Google and/or leave a comment).  You can also get an invite for and run it there. You can run it by opening a terminal and typing "python".

Things to play around with (once you have it running): change the starting geometry, step size (c), number of steps (n_steps), try printing out the geometry, energy and gradient for each step.

You can also try to write a similar program for other molecules (like methane), although once you have van der Waals interactions you will probably have to switch to Cartesian coordinates and things get complicated.

Related blog posts
The force is strong in this one
The autoopt tool in Avogadro

Wednesday, July 17, 2013

MOPAC/PCM interface in GAMESS

A new version of GAMESS was released recently.  Among the many new features is +Casper Steinmann's recent work on interfacing the PCM solvation method with the semiempirical methods AM1 and PM3.  So you can now simulate molecules in solution with AM1 and PM3.  

Casper also parallelized AM1 and PM3 (both in gas phase and solution), though molecules have to be pretty big before you see an appreciable speed up, as you can see from the figure below (on small proteins).

Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 

Monday, July 1, 2013

Computational Chemistry Highlights: June issue

The June issue of Computational Chemistry Highlights is out.

CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here.

Table of content for this issue features contributions from CCH editors Steven Bachrach, Jonathan Goodman, and Jan Jensen: