choderalab/openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

Language: Python - Size: 33 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 278 - Forks: 86

rinikerlab/reeds

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.

Language: Python - Size: 77.6 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 31 - Forks: 9

wehs7661/ensemble_md

A python package for performing GROMACS simulation ensembles

Language: Python - Size: 28.5 MB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 13 - Forks: 4

joabron/parallel-nanoalloys

A parallel molecular dynamics simulation algorithm for studying the thermal stability of nanoalloys.

Language: Python - Size: 129 KB - Last synced at: 7 months ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

wehs7661/enhanced_sampling_tutorials

A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS

Language: Jupyter Notebook - Size: 4.93 MB - Last synced at: 9 months ago - Pushed at: 10 months ago - Stars: 11 - Forks: 2

haoyangzheng1996/r2SGLD

The GitHub repository for "Constrained Exploration via Reflected Replica Exchange Stochastic Gradient Langevin Dynamics", ICML 2024

Language: Python - Size: 51.8 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 2 - Forks: 1

wehs7661/REMD_analysis

A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations

Language: Python - Size: 11.4 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 5

wehs7661/sampling_simulator

A python package for simulating sampling behaviors of enhanced sampling simulations

Language: Python - Size: 1.26 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

jear2412/BUQ-ODEsMCMC

Examples of several Markov Chain Monte Carlo methods such as t walk, emcee,Hamiltonian MC, Parallel Tempering HMC applied to UQ in ODEs

Language: Jupyter Notebook - Size: 10.1 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 4 - Forks: 1

matsunagalab/paper_higashida2021

Language: Rich Text Format - Size: 175 MB - Last synced at: 5 months ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 1

WayneDW/Variance_Reduced_Replica_Exchange_SGMCMC

Variance reduction in energy estimators accelerates the exponential convergence in deep learning (ICLR'21)

Language: C - Size: 265 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 3

JaydevSR/ReplicaExchangeMD.jl

Replica Exchange Molecular Dynamics (GSoC 2022 Project)

Language: Julia - Size: 15.9 MB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 0

snsinfu/f95-replica-exchange

Simple replica-exchange Langevin dynamics in Fortran 95 that samples from a one-dimensional multi-stable potential surface.

Language: Jupyter Notebook - Size: 54.7 KB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0

larsgeb/MPI_MC3

MC3 RWMH using MPI.

Language: C++ - Size: 51.8 KB - Last synced at: about 2 months ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0