Introducing sampling entropy in repository based adaptive umbrella sampling.
Determining free energy surfaces along chosen reaction coordinates is a common and important task in simulating complex systems. Due to the complexity of energy landscapes and the existence of high barriers, one widely pursued objective to develop efficient simulation methods is to achieve uniform sampling among thermodynamic states of interest. In this work, we have demonstrated sampling entropy (SE) as an excellent indicator for uniform sampling as well as for the convergence of free energy simulations. By introducing SE and the concentration theorem into the biasing-potential-updating scheme, we have further improved the adaptivity, robustness, and applicability of our recently developed repository based adaptive umbrella sampling (RBAUS) approach [H. Zheng and Y. Zhang, J. Chem. Phys. 128, 204106 (2008)]. Besides simulations of one dimensional free energy profiles for various systems, the generality and efficiency of this new RBAUS-SE approach have been further demonstrated by determining two dimensional free energy surfaces for the alanine dipeptide in gas phase as well as in water.
Zheng
Han
H
Department of Chemistry, New York University, New York, New York 10003, USA.
Zhang
Yingkai
Y
D000465:Algorithms; D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry*; D019277:Entropy; D008956:Models, Chemical; D014867:Water / Q000737:chemistry
D004151:Dipeptides; D014867:Water; C002956:alanylalanine