Andrea Rizzi's repositories
tfep-revisited-2021
Source code and input files associated to the paper "Targeted free energy perturbation revisited: Accurate free energies from mapped reference potentials".
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
alchemical-best-practices
Best practice document for alchemical free energy calculations going to livecoms journal
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
kinase-benchmark
Benchmark Yank against kinases and FDA approved inhibitors.
mcce-charges
generating ligand charges
mlcvs
Machine learning collective variables for enhanced sampling
openmmmcmc
MCMC sampler classes for OpenMM
openmmtools
Test systems for OpenMM
paper-microfluidics
Experiments with paper-based microfluidics
SAMPL6
Challenge inputs and details for the SAMPL6 challenge