metadynamics
There are 4 repositories under metadynamics topic.
crest-lab / crest
CREST - A program for the automated exploration of low-energy molecular chemical space.
Language:Fortran 198NNairIITK / Enhanced_Sampling_Methods_Tutorials
Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..
Language:Shell 40amirhajibabaei / AutoForce
Sparse Gaussian Process Potentials
Language:Python 27msultan / SML_CV
Using supervised machine learning to build collective variables for accelerated sampling
Language:Jupyter Notebook 27- Language:Python 24
sbhakat / AF-cryptic-pocket
Cryptic pocket prediction using AlphaFold 2
Language:Jupyter Notebook 22- Language:Shell 12
RedesignScience / cvpack
Useful Collective Variables for OpenMM
Language:Python 11wehs7661 / advanced_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 11Jan8be / metadynminer.py
Python package for efficient analysis of HILLS files generated by Plumed metadynamics simulations. Inspired by the Metadynminer package for R.
Language:Python 9KesPatil / ALK_files_2021_PNAS
This GitHub repo has folders required for setting up the Molecular Dynamics simulations, Metadynamics simulations, and a description of the post-processing codes that were used in the Patil et. al. PNAS 2021
Language:Jupyter Notebook 6- Language:Python 6
- Language:Python 5
How one can use binary classifiers, variational auto-encoder, TICA, PCA, distance and dihedral order parameters as CVs in context of pepsin-like aspartic proteases e.g. BACE1 and plasmepsin-II.
Language:Jupyter Notebook 4- Language:Jupyter Notebook 4
valsson-group / time-from-biased-simulations-tools
Simple tools for obtaining time from biased molecular dynamics simulations
Language:Python 4danieljsharpe / metadynamics
C++ implementation of metadynamics simulation on a potential energy surface
Language:C++ 3- Language:Roff 3
hejops / metadynamics
Run metadynamics simulations and analyse free energy surfaces
Language:Python 2ravenswing / mdsaps
Molecular Dynamics - Simulation Analysis and Preparation Suite
Language:Python 2tICA to capture local loop motion. Describes how to analyse loop movement using TICA and how to run PT-Metad using TIC vectors
Language:Jupyter Notebook 2Binary classifier as CV in enhanced sampling
Language:Jupyter Notebook 2- Language:Python 2
symbolic collective variable definitions and automation of metadynamics
Language:Python 1rangsimanketkaew / deepcv
Deep learning for collective variables.
Language:Python 1Auxiliary tools and scripts initially made for my PhD projects.
Language:Jupyter Notebook 1- Language:Python 1
ucl-tspptis / TS-PPTIS
New implementation of TS-PPTIS working with Gromacs 5.X and Plumed 2.X
Language:Python 1A repository for the test systems for the development of alchemical metadynamics
Language:Python 1A python package for simulating sampling behaviors of enhanced sampling simulations
Language:Python 1Peppone98 / Simulations_Recoverin
Standard molecular dynamics and metadynamics simulations of the Recoverin protein.
Language:Jupyter Notebook 0ianrgraham / hoomd-mimse
GPU-accelerated metadynamics code for obtaining low energy states
Language:Python
