In this paper, we illustrate a practical technique to improve the efficiency of the so-called multiple Bennett acceptance ratio (MBAR) estimator [Shirts and Chodera, J. Chem. Phys.129, 124105 (Year: 2008)] for computing thermodynamic expectations of physical quantities, from samples drawn from Hamiltonian or temperature replica exchange simulations. The methods exploit the Crooks fluctuation theorem[Crooks, J. Stat. Phys.90, 1481 (Year: 1998)] for accurately evaluating the partition functions ratios of neighboring replicas, thus providing an excellent initial guess for the MBAR iterative procedure.
Multiple Bennett acceptance ratio made easy for replica exchange simulations / Piero Procacci. - In: THE JOURNAL OF CHEMICAL PHYSICS. - ISSN 0021-9606. - STAMPA. - 139:(2013), pp. 124105-1-124105-6. [10.1063/1.4821814]
Multiple Bennett acceptance ratio made easy for replica exchange simulations
PROCACCI, PIERO
2013
Abstract
In this paper, we illustrate a practical technique to improve the efficiency of the so-called multiple Bennett acceptance ratio (MBAR) estimator [Shirts and Chodera, J. Chem. Phys.129, 124105 (Year: 2008)] for computing thermodynamic expectations of physical quantities, from samples drawn from Hamiltonian or temperature replica exchange simulations. The methods exploit the Crooks fluctuation theorem[Crooks, J. Stat. Phys.90, 1481 (Year: 1998)] for accurately evaluating the partition functions ratios of neighboring replicas, thus providing an excellent initial guess for the MBAR iterative procedure.I documenti in FLORE sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.