GregorySchwing

water_forcefields

Openff xmls and mol2 files for water models commonly used in biological simulations.

cugraph

cuGraph - RAPIDS Graph Analytics Library

cuStreamComp

Efficient CUDA Stream Compaction Library

concurrentqueue

A fast multi-producer, multi-consumer lock-free concurrent queue for C++11

ConservedWaterSearch

Python module for identification of conserved water molecules from molecular dynamics trajectories.

darts

A python library for user-friendly forecasting and anomaly detection on time series.

deep-learning-slow-modes

Supporting data for the manuscript "Deep learning the slow modes for rare events sampling"

docker

Dockerfile templates for creating RAPIDS Docker Images

dpcpp-cuda-examples-docker

Extended_MV_algorithm

This repository contains different implementations of the Micali-Vazirani algorithm, and experiments to compare performance.

GHOAT.py

The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.

LiGAN

Deep generative models of 3D grids for structure-based drug discovery

mbuild

A hierarchical, component based molecule builder

MV-matching

One-file C++ implementation of MV matching algorithm

pmda

Parallel algorithms for MDAnalysis

PYG_Examples

pytorch-forecasting

Time series forecasting with PyTorch

reproducibility_study

Repo for data collection, discussion, etc for a MoSDeF reproducibility study.

SALIENT

The official SALIENT system described in the paper "Accelerating Training and Inference of Graph Neural Networks with Fast Sampling and Pipelining".

SALIENT_plusplus

The official SALIENT++ system described in the paper "Communication-Efficient Graph Neural Networks with Probabilistic Neighborhood Expansion Analysis and Caching".

signac-flow

Workflow management for signac-managed data spaces.

SSTGraph

SYCL-For-CUDA-Examples

Examples for using SYCL on CUDA

syclacademy

SYCL Academy, a set of learning materials for SYCL heterogeneous programming

torchmd

End-To-End Molecular Dynamics (MD) Engine using PyTorch

TurboBFS

A highly scalable GPU-based set of top-down and bottom-up BFS algorithms in the language of  linear algebra.

vmd-packaging-instructions

Instructions for how to package VMD for Ubuntu and not pull your hair out in the process.

vmd_diffusion_coefficient

Computing Diffusion Coefficients in Macromolecular Simulations: The Diffusion Coefficient Tool for VMD

WaterNetworkAnalysis

Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis

wolfCalibration

Scripts for calibrating Alpha and RCutCoulomb for Wolf Summation