Rapid estimation of electronic degrees of freedom in Monte Carlo calculations for polarizable models of liquid water

2001 ◽  
Vol 114 (21) ◽  
pp. 9337-9349 ◽  
Author(s):  
Michael W. Mahoney ◽  
William L. Jorgensen
Keyword(s):  
Monte Carlo ◽  
Liquid Water ◽  
Degrees Of Freedom ◽  
Rapid Estimation ◽  
Monte Carlo Calculations

Erratum: Radiolysis of liquid water: An attempt to reconcile Monte-Carlo calculations with new experimental hydrated electron yield data at early times

2002 ◽  
Vol 80 (12) ◽  
pp. 1716
Author(s):  
Yusa Muroya ◽  
Jintana Meesungnoen ◽  
Jean-Paul Jay-Gerin ◽  
Abdelali Filali-Mouhim ◽  
Thomas Goulet ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Liquid Water ◽  
Hydrated Electron ◽  
Yield Data ◽  
Monte Carlo Calculations ◽  
Electron Yield

Reversibly Sampling Conformations and Binding Modes Using Molecular Darting

2020 ◽  
Author(s):  
Samuel C. Gill ◽  
David Mobley
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Binding Sites ◽  
Degrees Of Freedom ◽  
Dynamics Simulation ◽  
Hiv Integrase ◽  
Binding Modes ◽  
System A ◽  
Multiple Binding ◽  
Internal Degrees Of Freedom

<div>Sampling multiple binding modes of a ligand in a single molecular dynamics simulation is difficult. A given ligand may have many internal degrees of freedom, along with many different ways it might orient itself a binding site or across several binding sites, all of which might be separated by large energy barriers. We have developed a novel Monte Carlo move called Molecular Darting (MolDarting) to reversibly sample between predefined binding modes of a ligand. Here, we couple this with nonequilibrium candidate Monte Carlo (NCMC) to improve acceptance of moves.</div><div>We apply this technique to a simple dipeptide system, a ligand binding to T4 Lysozyme L99A, and ligand binding to HIV integrase in order to test this new method. We observe significant increases in acceptance compared to uniformly sampling the internal, and rotational/translational degrees of freedom in these systems.</div>

Monte Carlo calculations of neutron spectrum parameters at the JRTR NAA channels

2021 ◽  
Vol 134 ◽  
pp. 103688
Author(s):  
Ihsan Farouki ◽  
Rashdan Malkawi ◽  
Sayel Marashdeh
Keyword(s):  
Monte Carlo ◽  
Neutron Spectrum ◽  
Monte Carlo Calculations
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