BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation

2017 ◽  
Vol 19 (23) ◽  
pp. 15005-15020 ◽  
Author(s):  
Zhao X. Sun ◽  
Xiao H. Wang ◽  
John Z. H. Zhang
Keyword(s):  
Free Energy ◽  
Importance Sampling ◽  
Adaptive Sampling ◽  
Variance Minimization ◽  
Sampling Regime ◽  
Energy Simulations ◽  
Alchemical Free Energy

The efficiency of alchemical free energy simulations with a staging strategy is improved by adaptively manipulating the significance of each ensemble followed by importance sampling.

scholarly journals FESetup: Automating Setup for Alchemical Free Energy Simulations

2015 ◽  
Vol 55 (12) ◽  
pp. 2485-2490 ◽  
Author(s):  
Hannes H. Loeffler ◽  
Julien Michel ◽  
Christopher Woods
Keyword(s):  
Free Energy ◽  
Energy Simulations ◽  
Alchemical Free Energy

BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification

2018 ◽  
Vol 20 (3) ◽  
pp. 2009-2021 ◽  
Author(s):  
Xiaohui Wang ◽  
Xingzhao Tu ◽  
John Z. H. Zhang ◽  
Zhaoxi Sun
Keyword(s):  
Adaptive Sampling ◽  
Current Work ◽  
Variance Minimization ◽  
Acceptance Ratio ◽  
Bennett Acceptance Ratio ◽  
Sampling Regime

Following the previously proposed equilibrate-state sampling based adaptive sampling regime Optimum Bennett Acceptance Ratio (OBAR), we introduce its nonequilibrium extension, Optimum Crooks’ Equation (OCE) in the current work.

Chaperoned alchemical free energy simulations: A general method for QM, MM, and QM/MM potentials

2004 ◽  
Vol 120 (20) ◽  
pp. 9450-9453 ◽  
Author(s):  
Wei Yang ◽  
Ryan Bitetti-Putzer ◽  
Martin Karplus
Keyword(s):  
Free Energy ◽  
Energy Simulations ◽  
Alchemical Free Energy ◽  
General Method
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