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 koding.com and run it there. You can run it by opening a terminal and typing "python Emin.py".

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.

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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).

The work has been published in the open access journal PLoS ONE. +Jimmy Charnley Kromann is hard at work on implementing PM6.

This work is licensed under a Creative Commons Attribution 3.0 

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:

Molecularspace.org

Three interesting recent Angew. Chem. papers

Unraveling the Enigmatic Mechanism of L‐Asparaginase II with QM/QM calculations

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The 2013 Bjerrum-Brønsted-Lang Lecture: quantum biochemistry and the rise of semiempirical methods and automation in quantum chemistry

2013.06.29 UPDATE: Here's a recording of my talk.  Some more details: I received the A. Tovborg Jensen Award from the Royal Danish Academy of Sciences.  Tovborg Jensen was a Danish chemist who brought crystallography, which he learned from Bragg himself, to Denmark. Upon his death he bequeathed a considerable sum of money to the Royal Danish Academy of Sciences to establish the award and associated lecture series names in honor of his colleagues Niels Bjerrum (he of the Bjerrum length), Johannes Brønsted (Brønsted acid/base theory) and Kaj Linderstrøm-Lang (who coined the terms primary, secondary, tertiary and quaternary protein structure).



This afternoon I am giving the 2013 Bjerrum-Brønsted-Lang Lecture at the University of Copenhagen.  Here are my slides.  I plan to record the talk (using my iPhone) which I will post later.

The 2013 Bjerrum-Brønsted-Lang Lecture: quantum biochemistry and the rise of semiempirical methods and automation in quantum chemistry from molmodbasics

Illustrating EFMO fragmentation with Jmol

On Tuesday I am giving a talk and I want to illustrate fragmentation of a protein for the EFMO method.  So I used Jmol to create this movie which I will embed in a Powerpoint slide

The underlying Jmol script is here.  Just paste it in to the Jmol Script Console and record the screen (I used Screenflow, but screencast-o-matic is a free alternative).


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

Molecular Modeling Basics Reviewed on Amazon

Two reviews have appeared on Amazon: one on the Canadian site and one on the American site.  The latter one compares and contrasts MMB to Hincliffe's Molecular Modeling for Beginners.  As always, much appreciated!

Computational Chemistry Highlights: May issue

The May 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, Dan Gezelter, and Jan Jensen:

Describing Noncovalent Interactions beyond the Common Approximations: How Accurate Is the “Gold Standard,” CCSD(T) at the Complete Basis Set Limit?

The Optical Rotation of Methyloxirane in Aqueous Solution: A Never Ending Story?

Corrected small basis set Hartree-Fock method for large systems

The solution to the challenge in "Time-Reversible Random Number Generators" by Wm. G. Hoover and Carol G. Hoover

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