enhanced-sampling
There are 44 repositories under enhanced-sampling topic.
plumed/plumed2
Development version of plumed 2
Colvars/colvars
Collective variables library for molecular simulation and analysis programs
molmod/psiflow
scalable molecular simulation
luigibonati/mlcolvar
A unified framework for machine learning collective variables for enhanced sampling simulations
SSAGESLabs/PySAGES
Python Suite for Advanced General Ensemble Simulations
SSAGESproject/SSAGES
Software Suite for Advanced General Ensemble Simulations
ADicksonLab/wepy
Weighted Ensemble simulation framework in Python
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.
msultan/vde_metadynamics
Enhanced protein mutational sampling using time-lagged variational autoencoders
msultan/SML_CV
Using supervised machine learning to build collective variables for accelerated sampling
craabreu/ufedmm
Unified Free Energy Dynamics (UFED) simulations with OpenMM
danieljsharpe/DISCOTRESS
🦜 DISCOTRESS 🦜 is a software package to simulate and analyse the dynamics on arbitrary Markov chains
msultan/tf_metadynamics
Using neural networks for enhanced sampling in computational biophysics
RedesignScience/cvpack
Useful Collective Variables for OpenMM
bio-phys/asyncmd
asyncmd is a library to write concurrent code for setup, run and analysis of molecular dynamics simulations using pythons async/await synthax.
craabreu/openmm-nonbonded-slicing
An OpenMM plugin for slicing nonbonded interactions based on particle classification
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.
Ferg-Lab/pines
Permutationally invariant networks for enhanced sampling (PINES)
aakognole/rna-mg-predictor
Prediction of magnesium binding sites in RNA molecules using GCMC/MD (Updated version: https://github.com/mackerell-lab/GCMC_PME)
SSAGESLabs/openmm-dlext
Plugin for OpenMM providing simulation data wrappers as DLPack data structures
valsson-group/masterclass-22-11
Files for PLUMED Masterclass-22-11
valsson-group/time-from-biased-simulations-tools
Simple tools for obtaining time from biased molecular dynamics simulations
craabreu/openxps
Extended Phase-Space Simulations with OpenMM
danieljsharpe/metadynamics
C++ implementation of metadynamics simulation on a potential energy surface
Ferg-Lab/activeLearningPFASLinear
Data-driven discovery of linear molecular probes with optimal selective affinity for PFAS in water
SSAGESLabs/hoomd-dlext
Wrapper for HOOMD-blue simulation data into DLPack data structures
ves-code/plumed2-ves
Development version of PLUMED 2 which includes the VES code for performing variationally enhanced sampling simulations
SSAGESLabs/lammps-dlext
Wrapper for LAMMPS simulation data into DLPack data structures
weiHelloWorld/plumed_additional
Additional plumed plugins
apallath/pyves
Variationally enhanced sampling for single-particle langevin dynamics with neural network bias potentials and path collective variables. Based on OpenMM + PyTorch.
buenfilstats/Molecular-Dynamics-Project
Code and example notebook demostrating usage of Tangent Space Least Adaptive Clustering algorithm for molecular dynamics simulations with known collective variables
lexin-chen/WESTPA2.0-NAMD
WESTPA modified scripts with NAMD
rangsimanketkaew/deepcv
Deep learning for collective variables.
wehs7661/sampling_simulator
A python package for simulating sampling behaviors of enhanced sampling simulations