Development version of plumed 2
The d-SEAMS C++ core engine
Using supervised machine learning to build collective variables for accelerated sampling
Various integrations to the Schrodinger ecosystem. With major interest on analysis tools for Molecular Dynamics simulations run with Desmond.
Python package for efficient analysis of HILLS files generated by Plumed metadynamics simulations. Inspired by the Metadynminer package for R.
Using neural networks for enhanced sampling in computational biophysics
Fast estimation of ion-pairing for screening electrolytes
Permutationally invariant networks for enhanced sampling (PINES)
Run metadynamics simulations and analyse free energy surfaces
A package that allows you to read COLVAR output from Plumed and access data
Force-kernel eABF: a PLUMED enhanced-sampling plugin that delivers smooth mean-force estimates and free-energy landscapes from the earliest stages of sampling.
Additional plumed plugins
Simulate interactions between two fully-charged PAA chains with varying amounts of CaCl2 added
PLUMED-patched GROMACS molecular dynamics simulations repository used for my anti-scaling research project in the Wang Group.
Tools for STEM academic researchers
Reproducible MD + metadynamics re-analysis of the Trp rotamer switch in EMAP II (GROMACS, PLUMED, MDAnalysis, scikit-learn)
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