12 citations · 20 across the 5 of their papers we have counts for
5 papers
From populations to absolute binding affinities in molecular simulations: exact volumetric terms and practical estimators
Davide Mandelli, Emiliano Ippoliti, Charles Plate
We present a statistical-mechanics framework for computing equilibrium binding constants in the dilute limit. From first principles, we derive a general expression relating …
Extreme scaling of the metadynamics of paths algorithm on the pre-exascale JUWELS Booster supercomputer
Nitin Malapally, Marta Devodier, Giulia Rossetti +2
Molecular dynamics (MD)-based path sampling algorithms are a very important class of methods used to study the energetics and kinetics of rare (bio)molecular events. They sample th…
MiMiC: A High-Performance Framework for Multiscale Molecular Dynamics Simulations
Andrej Antalík, Andrea Levy, Sonata Kvedaravičiūtė +13
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory.…
Effective Data-Driven Collective Variables for Free Energy Calculations from Metadynamics of Paths
Lukas Müllender, Andrea Rizzi, Michele Parrinello +2
A variety of enhanced sampling methods predict multidimensional free energy landscapes associated with biological and other molecular processes as a function of a few selected coll…
A modified nudged elastic band algorithm with adaptive spring lengths
Davide Mandelli, Michele Parrinello
We present a modified version of the nudged elastic band (NEB) algorithm to find minimum energy paths con-necting two known configurations. We show that replacing the harmonic band…