enhanced-sampling
There are 9 repositories under enhanced-sampling topic.
- Language:C++ 319
- Language:C++ 192
- SSAGES
SSAGESproject / SSAGES
Software Suite for Advanced General Ensemble Simulations
Language:C++ 81 luigibonati / mlcolvar
A unified framework for machine learning collective variables for enhanced sampling simulations
Language:Python 80- PySAGES
SSAGESLabs / PySAGES
Python Suite for Advanced General Ensemble Simulations
Language:Python 51 ADicksonLab / wepy
Weighted Ensemble simulation framework in Python
Language:Python 48msultan / vde_metadynamics
Enhanced protein mutational sampling using time-lagged variational autoencoders
Language:Python 28Using supervised machine learning to build collective variables for accelerated sampling
Language:Jupyter Notebook 27rinikerlab / 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 27danieljsharpe / DISCOTRESS
🦜 DISCOTRESS 🦜 is a software package to simulate and analyse the dynamics on arbitrary Markov chains
Language:C++ 24- Language:Python 22
Using neural networks for enhanced sampling in computational biophysics
Language:Jupyter Notebook 14bio-phys / asyncmd
asyncmd is a library to write concurrent code for setup, run and analysis of molecular dynamics simulations using pythons async/await synthax.
Language:Python 8RedesignScience / cvpack
Useful Collective Variables for OpenMM
Language:Python 8craabreu / openmm-nonbonded-slicing
An OpenMM plugin for slicing nonbonded interactions based on particle classification
Language:C++ 7- Language:C++ 5
pedrojuanbj / MLTSA
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.
Language:Jupyter Notebook 5- Language:Python 5
aakognole / rna-mg-predictor
Prediction of magnesium binding sites in RNA molecules using GCMC/MD (Updated version: https://github.com/mackerell-lab/GCMC_PME)
Language:Shell 4- Language:Jupyter Notebook 4
valsson-group / time-from-biased-simulations-tools
Simple tools for obtaining time from biased molecular dynamics simulations
Language:Python 4- Language:Python 3
ves-code / plumed2-ves
Development version of PLUMED 2 which includes the VES code for performing variationally enhanced sampling simulations
Language:C++ 3C++ implementation of metadynamics simulation on a potential energy surface
Language:C++ 2Wrapper for HOOMD-blue simulation data into DLPack data structures
Language:C++ 2Plugin for OpenMM providing simulation data wrappers as DLPack data structures
Language:C++ 2weiHelloWorld / plumed_additional
Additional plumed plugins
Language:C++ 2apallath / pyves
Variationally enhanced sampling for single-particle langevin dynamics with neural network bias potentials and path collective variables. Based on OpenMM + PyTorch.
Language:Python 1buenfilstats / Molecular-Dynamics-Project
Code and example notebook demostrating usage of Tangent Space Least Adaptive Clustering algorithm for molecular dynamics simulations with known collective variables
- Language:Python 1
Ferg-Lab / activeLearningPFASLinear
Data-driven discovery of linear molecular probes with optimal selective affinity for PFAS in water
Language:Jupyter Notebook 1lexin-chen / WESTPA2.0-NAMD
WESTPA modified scripts with NAMD
Language:Shell 1rangsimanketkaew / deepcv
Deep learning for collective variables.
Language:Python 1wehs7661 / sampling_simulator
A python package for simulating sampling behaviors of enhanced sampling simulations
Language:Python 1- Language:JavaScript 0
Platform-agnostic OpenMM Forces
Language:C++ 0
