Replica Exchange Molecular Dynamics (GSoC 2022 Project)
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Updated
Aug 29, 2022 - Julia
Replica Exchange Molecular Dynamics (GSoC 2022 Project)
MC3 RWMH using MPI.
Simple replica-exchange Langevin dynamics in Fortran 95 that samples from a one-dimensional multi-stable potential surface.
A parallel molecular dynamics simulation algorithm for studying the thermal stability of nanoalloys.
A python package for simulating sampling behaviors of enhanced sampling simulations
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 Monte Carlo using PyStan2
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)
A python package for performing GROMACS simulation ensembles
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 repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
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