15 skills found
amirhajibabaei / AutoForceSparse Gaussian Process Potentials
Jan8be / Metadynminer.pyPython package for efficient analysis of HILLS files generated by Plumed metadynamics simulations. Inspired by the Metadynminer package for R.
dlukauskis / Funnel MakerFunnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.
choderalab / Kinase MetadynamicsTo run metadynamics simulations using openMM (based on Peter Eastman's script)
sbhakat / Plotting MD MetadynamicsJupyter Notebook showing how to plot FES, histograms and time-series data using Matplotlib.
AfroditiMariaZaki / FunnelMetadynamicsAnalysisA jupyter notebook for the analysis of Funnel Metadynamics simulation data.
KesPatil / ALK Files 2021 PNASThis 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
tiwarylab / Driving And Characterizing Nucleation Of Urea And Glycine Polymorphs In WaterPLUMED Nest files for metadynamics simulations of urea and glycine nucleation in water
ndonyapour / Funnel MetadynamicsFunnel Metadynamics MD Simulations
chrispy67 / VisMetaDynamicsAn interactive tutorial to metadynamics and enhanced sampling techniques for molecular dynamics simulations
sbhakat / Infrequent MetadynamicsPrediction of transition time (kinetics) associated with aromatic ring flipping using infrequent metadynamics
apallath / PostmetadPython package for post-processing PLUMED metadynamics and OPES simulations.
weitse-hsu / Alchemical MetadynamicsA repository for maintaining the simulation files and analysis codes for the JCTC paper of alchemical metadynamics
hejops / MetadynamicsRun metadynamics simulations and analyse free energy surfaces
brykimjh / Degrader Permeability Ml3d MetaDPredicts passive permeability of bifunctional degraders using ML and 3D descriptors from metadynamics simulations. Includes RF, PLS, and SVM models with 2D/3D features. Highlights the role of IMHBs, radius of gyration, and 3D-PSA in bRo5 space.
