Increasing the
Efficiency of Ensemble Molecular Dynamics
Simulations with Termination of Unproductive Trajectories Identified
at Runtime
Posted on 2025-02-04 - 22:14
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 component utilizes early termination
of individual trajectories identified as unproductive in the sampling
of conformational space. The criteria for termination are derived
quantities such as collective variables (CVs) and secondary quantities
calculated from the time series of CVs. They are computed and applied
during the trajectory generation. The approach is illustrated with
simulations of the FS peptide and evaluated from comparisons between
the free energy surfaces calculated from ensembles of complete, unabridged
simulations with those obtained from ensembles in which ∼5–50%
of trajectories were terminated early. Our early termination approach
can optimize computational efficiency while achieving a robust representation
of conformational space.
CITE THIS COLLECTION
DataCiteDataCite
No result found
Marquez, Jack; Cuendet, Michel A.; Caino-Lores, Silvina; Estrada, Trilce; Deelman, Ewa; Weinstein, Harel; et al. (2025). Increasing the
Efficiency of Ensemble Molecular Dynamics
Simulations with Termination of Unproductive Trajectories Identified
at Runtime. ACS Publications. Collection. https://doi.org/10.1021/acs.jpca.4c05182