Multidimensional replica-exchange method for free-energy calculations

By Y. Sugita, A. Kitao, Y. O. I. F. M. Science, the Graduate University of the Advanced Studies, Kyoto University. 2000

796 citations recorded by the source corpus.

We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in the original replica-exchange method, pairs of replicas with different temperatures and/or different parameters of the potential energy are exchanged in the new algorithm. This greatly enhances the sampling of the conformational space and allows accurate calculations of free energy in a wide temperature range from a single simulation run, using the weighted histogram analysis method.

Subfields: Atomic and Molecular Physics, and Optics, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/884c1c313bb108060ee921f4687ff7b21f8c5ce7

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In Atomic and Molecular Physics, and Optics

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Citations in the corpus

Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview (2018, methodology): “Integrations of US with other enhanced sampling techniques are reported in the literature, such as the replica-exchange umbrella sampling method (REUS), where an umbrella potential is exchanged among replicas (Sugita et al., 2000; Kokubo et al., 2011).”
MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. (2004, methodology): “For example, umbrella type biasing potentials could be used to restrain the radius of gyration or the fraction of native contacts to different values in each replica and, in a more general case, multiple biases can be combined in two-dimensional or even higher-dimensional replica exchange simulation”
Scalable molecular dynamics on CPU and GPU architectures with NAMD. (2020, methodology): “These strategies include multi-canonical temperature and Hamiltonian tempering replica-exchange MD 111,130–132 (REMD) and bias-exchange window-swapping umbrella sampling 133 (BEUS).”
Accounting for receptor flexibility and enhanced sampling methods in computer aided drug design (2013, methodology): “The sampling in each individual window can be performed using conventional molecular dynamics (cMD) or employing enhanced sampling techniques such as Hamiltonian replica exchange (41,49).”
Standard binding free energies from computer simulations: What is the best strategy? (2012, methodology): “49 Thus, conformations reached easily in some windows but comparatively inaccessible in others can quickly be communicated across all windows.”