metadynamics
There are 32 repositories under metadynamics topic.
crest-lab/crest
CREST - A program for the automated exploration of low-energy molecular chemical space.
NNairIITK/Enhanced_Sampling_Methods_Tutorials
Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..
amirhajibabaei/AutoForce
Sparse Gaussian Process Potentials
msultan/SML_CV
Using supervised machine learning to build collective variables for accelerated sampling
craabreu/ufedmm
Unified Free Energy Dynamics (UFED) simulations with OpenMM
sbhakat/AF-cryptic-pocket
Cryptic pocket prediction using AlphaFold 2
ajaymur91/CLIPS
Fast estimation of ion-pairing for screening electrolytes
RedesignScience/cvpack
Useful Collective Variables for OpenMM
wehs7661/advanced_sampling_tutorials
A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS
Jan8be/metadynminer.py
Python package for efficient analysis of HILLS files generated by Plumed metadynamics simulations. Inspired by the Metadynminer package for R.
KesPatil/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
tlhr/plumology
Plumology - Tools to analyse biased molecular dynamics simulations
jcwang587/xdatbus
A Python package for enhancing VASP AIMD simulations and analysis
sbhakat/PAP-review-inputs
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.
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
danieljsharpe/metadynamics
C++ implementation of metadynamics simulation on a potential energy surface
NNairIITK/Vreco_CPMD
CPMD Free Energy Surface Reconstruction
hejops/metadynamics
Run metadynamics simulations and analyse free energy surfaces
ravenswing/mdsaps
Molecular Dynamics - Simulation Analysis and Preparation Suite
sbhakat/BPTI-TICA-waterdynamics
tICA to capture local loop motion. Describes how to analyse loop movement using TICA and how to run PT-Metad using TIC vectors
sbhakat/Classifier-CV-sampling
Binary classifier as CV in enhanced sampling
theavey/AutoMet
A package to help automate molecular dynamics calculations
amirhajibabaei/easy-meta-md
symbolic collective variable definitions and automation of metadynamics
rangsimanketkaew/deepcv
Deep learning for collective variables.
ravenswing/phd_tools
Auxiliary tools and scripts initially made for my PhD projects.
sbhakat/colvar
A package that allows you to read COLVAR output from Plumed and access data
ucl-tspptis/TS-PPTIS
New implementation of TS-PPTIS working with Gromacs 5.X and Plumed 2.X
wehs7661/MetaD_EXE_TestSys
A repository for the test systems for the development of alchemical metadynamics
wehs7661/sampling_simulator
A python package for simulating sampling behaviors of enhanced sampling simulations
Peppone98/Simulations_Recoverin
Standard molecular dynamics and metadynamics simulations of the Recoverin protein.
ianrgraham/hoomd-mimse
GPU-accelerated metadynamics code for obtaining low energy states