ChemRxiv
These are preliminary reports that have not been peer-reviewed. They should not be regarded as conclusive, guide clinical practice/health-related behavior, or be reported in news media as established information. For more information, please see our FAQs.
1/1
2 files

Exploring Protocols to Build Reservoirs to Accelerate Replica Exchange MD Simulations

preprint
submitted on 19.05.2020, 14:30 and posted on 20.05.2020, 09:16 by koushik kasavajhala, kenneth lam, Carlos Simmerling
Replica Exchange Molecular Dynamics (REMD) is a widely used enhanced sampling method for accelerating biomolecular simulations. During the past two decades, several variants of REMD have been developed to further improve the rate of conformational sampling of REMD. One such variant, Reservoir REMD (RREMD), was shown to improve the rate of conformational sampling by around 5-20x. Despite the significant increase in sampling speed, RREMD methods have not been widely used due to the difficulties in building the reservoir and also due to the code not being available on the GPUs.

In this work, we ported the AMBER RREMD code onto GPUs making it 20x faster than the CPU code. Then, we explored protocols for building Boltzmann-weighted reservoirs as well as non-Boltzmann reservoirs, and tested how each choice affects the accuracy of the resulting RREMD simulations. We show that, using the recommended protocols outlined here, RREMD simulations can accurately reproduce Boltzmann-weighted ensembles obtained by much more expensive conventional REMD simulations, with at least 15x faster convergence rates even for larger proteins (>50 amino acids) compared to conventional REMD.

Funding

NIH #GM107104

History

Email Address of Submitting Author

koushik.sbiiit@gmail.com

Institution

Stony Brook University

Country

USA

ORCID For Submitting Author

0000-0002-5040-0518

Declaration of Conflict of Interest

The authors declare no competing financial interest

Exports