QM/MM Alchemical Free Energy Simulations: Challenges and Recent Developments

2010 ◽  
pp. 51-62 ◽  
Author(s):  
Wei Yang ◽  
Qiang Cui ◽  
Donghong Min ◽  
Hongzhi Li
Keyword(s):  
Free Energy ◽  
Recent Developments ◽  
Energy Simulations ◽  
Alchemical Free Energy

scholarly journals Recent developments in multiscale free energy simulations

2022 ◽  
Vol 72 ◽  
pp. 55-62
Author(s):  
Emilia P. Barros ◽  
Benjamin Ries ◽  
Lennard Böselt ◽  
Candide Champion ◽  
Sereina Riniker
Keyword(s):  
Free Energy ◽  
Recent Developments ◽  
Energy Simulations

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

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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