andrrizzi

tfep-revisited-2021

Source code and input files associated to the paper "Targeted free energy perturbation revisited: Accurate free energies from mapped reference potentials".

tfep

A library to perform targeted free energy perturbation with normalizing flows.

paper-multimap-tfep-2023

Source code and input files associated to the paper "Multimap targeted free energy estimation"

model-missing

Script to automatically add missing residues and refine loops with MODELLER

MSE

Just a personal repo to play around with molecular simulations.

phd-thesis

alchemical-best-practices

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

robots

Laboratory automation toolkits

alchemy

Alchemical tools for OpenMM

andrrizzi.github.io

Somewhat more than a cheat sheet that gets updated with me.

benchmarksets

Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards

clusterutils

Utilities for running parallel jobs with Torque/Moab and MPI

conda-recipes

conda build recipes for the Omnia project

goodiebag

kinase-benchmark

Benchmark Yank against kinases and FDA approved inhibitors.

mcce-charges

generating ligand charges

mdtraj

A modern, open library for the analysis of molecular dynamics trajectories

mlcvs

Machine learning collective variables for enhanced sampling

openmm

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

openmmmcmc

MCMC sampler classes for OpenMM

openmmtools

Test systems for OpenMM

openmoltools

paper-microfluidics

Experiments with paper-based microfluidics

repex

Python replica-exchange simulation facility for OpenMM.

SAMPL6

Challenge inputs and details for the SAMPL6 challenge

schema

Schema validation just got Pythonic

yank

GPU-accelerated calculation of ligand binding affinities in implicit and explicit solvent using alchemical free energy methodologies