Abstract

The application of molecular dynamics (MD) simulations to study increasingly larger and more complex systems is challenged by the required amounts of trajectory data needed to sample their conformational space appropriately. The analysis and interpretation phase of such massive data sets that have to be stored and fed to the various algorithms to reveal the dynamic behaviors of the systems and the underlying energetics in structural terms related to functional mechanisms are also a significant challenge. To develop computational means that can address these challenges, we are developing a software framework that can increase the efficiency of this process. We present one component of this framework that can reduce the size of the accumulating data set while maintaining the structural attributes, distribution, and relative probability ranking of the minima in the free energy map for the system. This framework …

Metadata

publication

The Journal of Physical Chemistry A, 2025

year

2025

publication date

2025/2

authors

Jack Marquez, Michel A Cuendet, Silvina Caino-Lores, Trilce Estrada, Ewa Deelman, Harel Weinstein, Michela Taufer

link

https://pubs.acs.org/doi/abs/10.1021/acs.jpca.4c05182

journal

The Journal of Physical Chemistry A

publisher

American Chemical Society