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openchem

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

openforcefield

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

optimus_bind_sample

Designed to optimize the time/accuracy trade-off in predicting the effects of mutations on protein-protein binding

packmem

packmem: a tool to compute interfacial packing defects in simulated membranes

papersindevel

Work that is in development, but ones I want to show.

polyply_1.0

Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates

programmingprojects

C++ Programming Tutorial in Chemistry

pteros

Modern and fast molecular analysis and modeling library for C++ and Python

pycgtool

Python tool for performing coarse-grain mapping and model generation from atomistic molecular dynamics trajectories.

pycontact

Analysis of non-covalent interactions in MD trajectories

pyemma

🚂 Python API for Emma's Markov Model Algorithms 🚂

pyod

A Python Toolkit for Scalable Outlier Detection (Anomaly Detection)

python-package-boilerplate

A starter kit for publishing a python package

pythonmdscripts

Folder containing the analysis code in C++/Python in MARTINI or SDK

research

PhD Molecular Dynamics Analysis Code - updated daily

rip-md

rustlibraries

sang_prefect

scf_szabo

This is a C version of the SCF code found in Appendix B of Modern Quantum Chemistry, An Introduction to Electronic Structure Theory by A. Szabo and N. Ostlund. I have included a built executable "scf_basic_version_1_0" and an output file called "out" which lists the results. Run the command "make" to build this. Note that this software is not designed to be either efficient in terms of performance or in terms of coding. It is designed as a bit of fun to convert the original Fortran IV code into something a bit more modern - C and also to demonstrate the key principles of the SCF routine when calculating the HeH+ molecule. Limited to STO-nG (n=1, 2 or 3) series basis set and 2 atoms only.

seaborn_in_r

How to make seaborn plots in R

simple-membrane-protein-analysis

This is a short tutorial showing how to use both VMD and MDAnalysis to analyse a molecular dynamics simulation of a membrane protein.

software-development

A primer on software development best practices for computational chemistry

stripednp_top_2019

Supplementary information regarding NP topologies in GROMACS

syn_cthw

C Practise as I am a bit rusty..

synjulia

timeseriescrossvalidation

Time-Series Cross-Validation Module

uclcollagengroup

Software, script and documentation repository for the UCL Collagen Group.

votca

VOTCA's next generation build system

website_testing

Testing django templates