scholarly journals Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment

2008 ◽  
Vol 128 (20) ◽  
pp. 205106 ◽  
Author(s):  
Xuhui Huang ◽  
Gregory R. Bowman ◽  
Vijay S. Pande
Keyword(s):  
Free Energy ◽  
Distributed Computing ◽  
Sampling Methods ◽  
Energy Landscapes ◽  
Enhanced Sampling ◽  
Computing Environment ◽  
Free Energy Landscapes ◽  
Folding Free Energy

scholarly journals Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin

2016 ◽  
Vol 113 (5) ◽  
pp. 1150-1155 ◽  
Author(s):  
Patrick Shaffer ◽  
Omar Valsson ◽  
Michele Parrinello
Keyword(s):  
Free Energy ◽  
Sampling Methods ◽  
Molecular Simulations ◽  
High Dimensionality ◽  
High Dimensional ◽  
Energy Landscapes ◽  
Enhanced Sampling ◽  
Collective Variables ◽  
Targeted Sampling ◽  
Free Energy Landscapes

The capabilities of molecular simulations have been greatly extended by a number of widely used enhanced sampling methods that facilitate escaping from metastable states and crossing large barriers. Despite these developments there are still many problems which remain out of reach for these methods which has led to a vigorous effort in this area. One of the most important problems that remains unsolved is sampling high-dimensional free-energy landscapes and systems that are not easily described by a small number of collective variables. In this work we demonstrate a new way to compute free-energy landscapes of high dimensionality based on the previously introduced variationally enhanced sampling, and we apply it to the miniprotein chignolin.

A topological order parameter for describing folding free energy landscapes of proteins

2018 ◽  
Vol 149 (17) ◽  
pp. 175101 ◽  
Author(s):  
Pham Dang Lan ◽  
Maksim Kouza ◽  
Andrzej Kloczkowski ◽  
Mai Suan Li
Keyword(s):  
Free Energy ◽  
Order Parameter ◽  
Topological Order ◽  
Energy Landscapes ◽  
Free Energy Landscapes ◽  
Folding Free Energy

Folding free energy landscapes of β-sheets with non-polarizable and polarizable CHARMM force fields

2018 ◽  
Vol 149 (7) ◽  
pp. 072317 ◽  
Author(s):  
Anthony J. Hazel ◽  
Evan T. Walters ◽  
Christopher N. Rowley ◽  
James C. Gumbart
Keyword(s):  
Free Energy ◽  
Force Fields ◽  
Energy Landscapes ◽  
Free Energy Landscapes ◽  
Β Sheets ◽  
Folding Free Energy
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