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alchemical-best-practices

Best practice document for alchemical free energy calculations going to livecoms journal

apocharmm

apocharmm-workshop

A series of tutorials for apoCHARMM workshop

basic_simulation_training

A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations (oriented towards molecular dynamics (MD)), providing some training itself and linking out to other helpful information elsewhere. The intent is that this provide information on the prerequisites which will be required for understanding/following many of the other "best practices" documents being prepared.

cpp14

This repository contains my tests of the features introduced in the c++14

cses

This repository contains my attempts at solving the problems in cses

cuda

This repository contains cuda code for my accompanying blog at https://stuffsrandom.wordpress.com

dsalgo

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

fastpages

gnn

gse

Gaussian Split Ewald and other non-PME electrostatics methods

hpka

jax-md

Differentiable, Hardware Accelerated, Molecular Dynamics

logp_prediction

#logP prediction model

mathematical_physics

An exploration of mathematical physics through python.

modulo7

A semantic and technical analysis of musical scores based on Information Retrieval Principles

ocaml_gpu

This repository is an exploratory attempt at a CUDA backend for OCaml

openmm

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

prml

PRML algorithms implemented in Python

pyparam

pytorch_graph_simulator

qmcode

Basic qm code development in python

ragan

Imaging, Machine Learning, Workflow

reinforcement_learning_bootcamp

This repository contains my attempts at going through the Deep RL Bootcamp

samar.github.io

samarjeet.github.io

sampl7

Challenge details, inputs, and results for the SAMPL7 series of challenges

testpybind11

uvadlc_notebooks

Repository of Jupyter notebook tutorials for teaching the Deep Learning Course at the University of Amsterdam (MSc AI), Fall 2021