A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.
A python package for performing GROMACS simulation ensembles
A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS
A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations
Variance reduction in energy estimators accelerates the exponential convergence in deep learning (ICLR'21)
The GitHub repository for "Constrained Exploration via Reflected Replica Exchange Stochastic Gradient Langevin Dynamics", ICML 2024
Examples of several Markov Chain Monte Carlo methods such as t walk, emcee,Hamiltonian MC, Parallel Tempering HMC applied to UQ in ODEs
Replica Exchange Molecular Dynamics (GSoC 2022 Project)
Replica Exchange Monte Carlo using PyStan2
Simple replica-exchange Langevin dynamics in Fortran 95 that samples from a one-dimensional multi-stable potential surface.
A python package for simulating sampling behaviors of enhanced sampling simulations
A parallel molecular dynamics simulation algorithm for studying the thermal stability of nanoalloys.
MC3 RWMH using MPI.
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