Techmint Blog: python

python

Showing posts with label python. Show all posts

572. autorotate/superimpose python script

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 xyz...

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

I suppose we can call it the VSPQM, which sounds a bit like a Roman initialism, akin to SPQR. I've spent the past few days trying to get...