enhanced-sampling

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.

python workflow hpc drug-design enhanced-sampling eds free-energy-calculations replica-exchange gromos

UpdatedFeb 18, 2024
Python

msultan /vde_metadynamics

Star29

Enhanced protein mutational sampling using time-lagged variational autoencoders

machine-learning deep-learning molecular-dynamics pytorch mutations auto-encoders enhanced-sampling

UpdatedSep 17, 2018
Python

msultan /SML_CV

Star28

Using supervised machine learning to build collective variables for accelerated sampling

machine-learning openmm supervised-learning enhanced-sampling plumed supervised-machine-learning metadynamics collective-variables accelerated-sampling

UpdatedJun 26, 2018
Jupyter Notebook

craabreu /ufedmm

Star27

Unified Free Energy Dynamics (UFED) simulations with OpenMM

molecular-dynamics openmm free-energy enhanced-sampling metadynamics collective-variables

UpdatedMar 9, 2024
Python

danieljsharpe /DISCOTRESS

Star25

🦜 DISCOTRESS 🦜 is a software package to simulate and analyse the dynamics on arbitrary Markov chains

markov-model simulation markov-chain kinetic-monte-carlo markov-chains stochastic-processes stochastic-simulation-algorithm markov-process random-walk ctmc enhanced-sampling stochastic-simulation dtmc network-dynamics rare-events k-shortest-paths markovian-dynamics continuous-time-markov-chain simulation-algorithms

UpdatedJul 29, 2021
C++

msultan /tf_metadynamics

Star16

Using neural networks for enhanced sampling in computational biophysics

neural-network pytorch computational-chemistry enhanced-sampling plumed

UpdatedAug 17, 2017
Jupyter Notebook

RedesignScience /cvpack

Star12

Useful Collective Variables for OpenMM

molecular-dynamics openmm enhanced-sampling metadynamics collective-variables

UpdatedMay 9, 2024
Python

bio-phys /asyncmd

Star11

asyncmd is a library to write concurrent code for setup, run and analysis of molecular dynamics simulations using pythons async/await synthax.

molecular-dynamics slurm molecular-dynamics-simulation slurm-cluster enhanced-sampling

UpdatedFeb 25, 2025
Python

craabreu /openmm-nonbonded-slicing

Star8

An OpenMM plugin for slicing nonbonded interactions based on particle classification

molecular-dynamics enhanced-sampling alchemical-free-energy

UpdatedDec 11, 2023
C++

Ferg-Lab /pines

Star6

Permutationally invariant networks for enhanced sampling (PINES)

molecular-simulation free-energy enhanced-sampling plumed collective-variables permutational-invariance

UpdatedAug 25, 2023
C++

pedrojuanbj /MLTSA

Star6

Machine Learning Transition State Analysis (MLTSA) suite with Analytical models to create data on demand and test the approach on different types of data and ML models.

machine-learning deep-learning time-series tensorflow sklearn molecular-dynamics sklearn-compatible enhanced-sampling time-series-analysis time-series-classification molecular-dynamics-analysis tensorflow-compatible