SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM 7.5 Molecular Dynamics Engine

16 August 2021, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


We present SEEKR2 (Simulation-Enabled Estimation of Kinetic Rates Version 2) – the latest iteration in the family of SEEKR programs for using multiscale simulation methods to computationally estimate the kinetics and thermodynamics of molecular processes, in particular, ligand-receptor binding. SEEKR2 generates equivalent, or improved, results compared to the earlier versions of SEEKR, but with significant increases in speed and capabilities. SEEKR2 has also been built with greater ease of usability with extensible features to enable future expansions of the method. Now, in addition to supporting simulations using NAMD, calculations may be run with the fast and extensible OpenMM simulation engine. The Brownian dynamics portion of the calculation has also been upgraded to Browndye 2.


Markovian Milestoning with Voronoi Tesselations
Molecular Dynamics
Brownian Dynamics
Simulation Enabled Estimation of Kinetic Rates

Supplementary materials

SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM 7.5 Molecular Dynamics Engine Supplementary Information
The supplementary information shows convergence data for the main manuscript.


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