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bioRxiv · 10.1101/2023.03.06.531337

OneOPES, a combined enhanced sampling method to rule them all

Rizzi, V.·Aureli, S.·Ansari, N.·Gervasio, F. L.
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Abstract

Enhanced sampling techniques have revolutionised molecular dynamics (MD) simulations, enabling the study of rare events and the calculation of free energy differences in complex systems. One of the main families of enhanced sampling techniques uses physical degrees of freedom called collective variables (CVs) to accelerate a systems dynamics and recover the original systems statistics. However, encoding all the relevant degrees of freedom in a limited number of CVs is challenging, particularly in large biophysical systems. Another category of techniques, such as parallel tempering, simulates multiple replicas of the system in parallel, with-out requiring CVs. However, these methods may explore less relevant high-energy portions of the phase space and become computationally expensive for large systems. To overcome the limitations of both approaches, we propose a replica exchange method called OneOPES that combines the power of multi-replica simulations and CV-based enhanced sampling. This method efficiently accelerates the phase space sampling without the need for ideal CVs, extensive parameters fine tuning nor the use of a large number of replicas, as demonstrated by its successful applications to protein-ligand binding and protein folding benchmark systems. Our approach shows promise as a new direction in the development of enhanced sampling techniques for molecular dynamics simulations, providing an efficient and robust framework for the study of complex and unexplored problems. Table of Content Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/531337v2_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@88b5ceorg.highwire.dtl.DTLVardef@15817deorg.highwire.dtl.DTLVardef@8721bforg.highwire.dtl.DTLVardef@1b8b314_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Rizzi, V., Aureli, S., Ansari, N., Gervasio, F. L.. 2023-03-07. OneOPES, a combined enhanced sampling method to rule them all. https://doi.org/10.1101/2023.03.06.531337

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