A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
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Updated
Apr 26, 2024 - Python
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 for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations
A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS
Variance reduction in energy estimators accelerates the exponential convergence in deep learning (ICLR'21)
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
MC3 RWMH using MPI.
A parallel molecular dynamics simulation algorithm for studying the thermal stability of nanoalloys.
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