Dual-Topology Hamiltonian-Replica-Exchange Overlap Histogramming Method to Calculate Relative Free Energy Difference in Rough Energy Landscape
Donghong Min, Hongzhi Li, Guohui Li, Ryan Bitter-Putzer, Wei Yang
Abstract
A novel overlap histogramming method based on Dual-Topology Hamiltonian-Replica-Exchange simulation technique is presented to efficiently calculate relative free energy difference in rough energy landscape, in which multiple conformers coexist and are separated by large energy barriers. The proposed method is based on the realization that both DT-HERM exchange efficiency and confidence of free energy determination in overlap histogramming method depend on the same criteria: neighboring states' energy derivative distribution overlap. In this paper, we demonstrate this new methodology by calculating free energy difference between amino acids: Leucine and Asparagine, which is an identified chanllenging system for free energy simulations.
Create a lesson
Related papers
Real-Time Emergence of Charge-Transfer-to-Solvent States from Core Excitation
Jiří Suchan, B. Scott Fales, Benjamin G. Levine et al.
ElemCo.jl: A Julia package for electron-correlation methods
Daniel Kats, Charlotte Rickert, Thomas Schraivogel et al.
Franson-Interferometric Bounds on Entangled Two-Photon Absorption
Albin Hedse, Sankaran Ramesh, Luis Matheis et al.
The off-diagonal low rank property: new opportunities for low-scaling computational chemistry methods
Zikuan Wang
Core-valence double ionization of SF6 involving S2p, F1s and S1s inner shells
Veronica Daver Ideböhn, Daniel M. Pereira, Lucas M. Cornetta et al.
Benchmark of Multi-Channel Dyson Equation and Algebraic Diagrammatic Construction Methods for molecules
Mike Keizer, Stefano Paggi, J. Arjan Berger et al.