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Molecular modeling software

11 Jul

One of the very useful things I’ve learned at DTU is how to use several kinds of molecular modeling and computational chemistry software. Among them are:

Spartan – commercial, but there’s a trial available. Can do molecular mechanics, semi-empirical methods, ab initio models, DFT methods, post Hartree-Fock methods, and quantum chem composite methods.

Pymol – free, open source, Python-based. Allows you to create pretty images of proteins.

VMD (Visual Molecular Dynamics) – open source and free to academics. A molecular visualization program for displaying, animating, and analyzing large biomolecular systems -f.ex., ligand-binding.

Schr̦dinger Suite, including Maestro, MacroModel, and Jaguar Рcommercial. Maestro is a nice, user-friendly, visual interface for molecular modeling and reaction simulation. Macromodel (accessible through Maestro) uses force field methods to calculate pretty accurate relative energies for your chemical systems. Even more powerful is Jaguar, which employs ab initio QM methods to characterize reactions mechanisms and transition states.


What’s that stuff?

8 Jul

This is kind of fun:

What’s That Stuff?

Which is better?

12 Jun

The plum pudding model or the muffin-tin approximation?

Chemistry blog!

11 Jun

Hello! Welcome to my new chemistry blog. I’ve been wanting to start such a blog for a while, but I hadn’t thought of a suitable titular pun. Here I’ll cover chemistry news, articles, chemistry in Denmark, websites, and random things that I think are interesting. I’m thinking it may be updated weekly or something like that.