Optimization of Monte Carlo trial moves for protein simulations

2011 ◽  
Vol 134 (1) ◽  
pp. 014104 ◽  
Author(s):  
Marcos R. Betancourt
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Trial

WANG–LANDAU SIMULATIONS OF ADSORBED AND CONFINED LATTICE PROTEINS

2012 ◽  
Vol 23 (08) ◽  
pp. 1240008 ◽  
Author(s):  
BUSARA PATTANASIRI ◽  
YING WAI LI ◽  
DAVID P. LANDAU ◽  
THOMAS WÜST
Keyword(s):  
Monte Carlo ◽  
Protein Folding ◽  
Protein Adsorption ◽  
Density Of States ◽  
Adsorption Behavior ◽  
Hp Model ◽  
Monte Carlo Trial ◽  
Lattice Proteins

The hydrophobic-polar (HP) model has emerged as one of the standard approaches for simulating protein folding. In this work, we used this model together with Wang–Landau (WL) sampling and appropriate Monte Carlo trial moves to determine the density of states and thermodynamics for two cases: Protein adsorption and protein confinement, in the vicinity of attractive surfaces. The influence on the adsorption behavior of surface attractive strength in the adsorption case and volumetric spaces in the confinement case will be discussed.

Quantum Monte Carlo study of first-row atoms using transcorrelated variational Monte Carlo trial functions

2007 ◽  
Vol 126 (16) ◽  
pp. 164109 ◽  
Author(s):  
Rajendra Prasad ◽  
Naoto Umezawa ◽  
Dominik Domin ◽  
Romelia Salomon-Ferrer ◽  
William A. Lester
Keyword(s):  
Monte Carlo ◽  
Quantum Monte Carlo ◽  
Monte Carlo Study ◽  
Variational Monte Carlo ◽  
Monte Carlo Trial

Efficient Monte Carlo trial moves for polypeptide simulations

2005 ◽  
Vol 123 (17) ◽  
pp. 174905 ◽  
Author(s):  
Marcos R. Betancourt
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Trial
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