An Implementation of Replica Exchange with Dynamical Scaling for Efficient Large-Scale Simulations

Rick, Steven W.; Schwing, Gregory J.; Summa, Christopher M.

doi:10.1021/acs.jcim.0c01236

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An Implementation of Replica Exchange with Dynamical Scaling for Efficient Large-Scale Simulations

Rick, Steven W.·Schwing, Gregory J.·Summa, Christopher M.

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Abstract

An implementation of the replica exchange with dynamical scaling (REDS) method in the commonly used molecular dynamics program GROMACS is presented. REDS is a replica exchange method that requires fewer replicas than conventional replica exchange while still providing data over a range of temperatures and can be used in either constant volume or constant pressure ensembles. Details for running REDS simulations are given, and an application to the human islet amyloid polypeptide (hIAPP) 11-25 fragment shows that the model efficiently samples conformational space.

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY Chemistry Computer science Computer simulations Energy Enthalpy Nucleic acid structure Peptides and protein Pharmacology and pharmacy

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Rick, Steven W., Schwing, Gregory J., Summa, Christopher M.. 2021-01-26. An Implementation of Replica Exchange with Dynamical Scaling for Efficient Large-Scale Simulations. https://doi.org/10.1021/acs.jcim.0c01236

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