If you want to calculate reaction coordinates between two structures you need to make sure that the structures haven't been rotated or t...

Most people who have used gaussian will be familiar with molecules that are rotated multiple times during optimisation. Occasionally,  the m...

Generating bond, angle and dihedral parameters for GROMACS molecular dynamics simulations is a real PITA when it comes to reasonably large a...

This is a silly little script -- ECCE, which I use to manage all my computations, is very particular about what XYZ files it can and cannot ...

What I'm showing here is probably overkill -- there may be better ways of doing this with sed/awk*. However, since I had most of the cod...

There are a few reasons to like gaussian, and many reasons not to. Gaussian is fast, and their whitepapers are great resources for learning...

Another update: It now dumps the energies in a file, energies.dat, as well. Update: some programmes, like ecce, are more picky about the...

Update 2: The coordinates are actually gradients, and so aren't terribly informative to a casual user like myself. See this post for how...

Many, many years ago I learned basic programming using BASIC (the version that came with PC DOS 5, I think). I even wrote the odd game, but ...

Rather naively I was hoping that by comparing two  molecule .xyz files and generating an average of them I would be able to conveniently gen...

This script does something I could easily do myself in e.g. bc , and so is a bit of a waste of time. However, because I enjoy writing short ...

UPDATED! I've moved the finished scripts to here: https://sourceforge.net/projects/nwbas2ecce/ They work! I've also added a num...

Here's the molecular weight part of the isotopic pattern calculator in a previous post. Most people won't need a full molecular ...