Pinned Repositories
alchemical-analysis
An open tool implementing some recommended practices for analyzing alchemical free energy calculations
bkit
compute_fep
Free energy perturbation for LAMMPS.
deeptime
Python library for analysis of time series data including dimensionality reduction, clustering, and Markov model estimation
ewald
InterMol
Conversion tool for molecular simulations
mdtraj
An open library for the analysis of molecular dynamics trajectories
msm_we
History-augmented Markov analysis of weighted ensemble trajectories.
SynD
Library for easily creating and using highly efficient, arbitrarily complex synthetic dynamics models
westpa2_tutorials
Tutorials and additional documentation for the WESTPA 2.0. (For future LiveCoMS Tutorial Paper)
jpthompson17's Repositories
jpthompson17/ewald
jpthompson17/msm_we
History-augmented Markov analysis of weighted ensemble trajectories.
jpthompson17/SynD
Library for easily creating and using highly efficient, arbitrarily complex synthetic dynamics models
jpthompson17/westpa2_tutorials
Tutorials and additional documentation for the WESTPA 2.0. (For future LiveCoMS Tutorial Paper)
jpthompson17/alchemical-analysis
An open tool implementing some recommended practices for analyzing alchemical free energy calculations
jpthompson17/bkit
jpthompson17/compute_fep
Free energy perturbation for LAMMPS.
jpthompson17/deeptime
Python library for analysis of time series data including dimensionality reduction, clustering, and Markov model estimation
jpthompson17/InterMol
Conversion tool for molecular simulations
jpthompson17/mdtraj
An open library for the analysis of molecular dynamics trajectories
jpthompson17/openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
jpthompson17/openmm_orion
Cubes and Floes for running MD on the OpenEye Cloud Computing Platform Orion
jpthompson17/ParmEd
Amber parameter topology file editor
jpthompson17/pudl
The Public Utility Data Liberation Project provides analysis-ready energy system data to climate advocates, researchers, policymakers, and journalists.
jpthompson17/PyEMMA
🚂 Python API for Emma's Markov Model Algorithms 🚂
jpthompson17/pymbar
Python implementation of the multistate Bennett acceptance ratio (MBAR)
jpthompson17/westpa
WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
jpthompson17/westpa_tutorials
Tutorials and additional documentation for the WESTPA suite