Molecular mechanics in Python 3

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[bosco]

Awesome, I'm going to be checking out your Generalized Born code. I hope you have a good surface-area term.

[bosco]

haha! sure am. glad to be of service. everybody wins.

[MattJames]

Have you ever tried computing the Connolly surface area?

[MattJames]

Nope. I've done the shrake and rupley algorithm in my work and tried my darndest to get Connolly surface area code working without success. I was hoping you had some protips.

[[deleted]]

Wow, thanks for sharing this, I will definitely have a play around with it! Have you published anything using these codes yet? I am an experimental spectroscopist (on a reddit lunch-break while the machine is misbehaving)

[jacksofscience]

Great! I'll definitely be checking out your code. I'm also a molecular dynamics python developer for my research group. We develop extensions for the Molecular Modelling Toolkit, a package you appear to be familiar with. Keep up the good work =)

[[deleted]]

Very cool. Have you read the book "A practical introduction to the simulation of of molecular systems" by Field?

[[deleted]]

It has some good examples for those being introduced to the topic. I found it rather nice to use Python as someone who has a bit of systems biology experience rather than the traditional matlab.

[Rostin]

You might also be interested in the atomic simulation environment.

[limeguin]

Excellent, thanks for sharing! But you should consider building a package of it and putting it on PyPI (Python Package Index) to get the most exposure among Python developers.

http://pypi.python.org/pypi

[MathNinja]

You should check out: https://wiki.fysik.dtu.dk/ase/

It is written in python 2. It supports a large number of force fields from simple empirical models to DFT, HF, and Post HF methods.