Calculation of Free Energy Profiles for Elementary Bimolecular Reactions by ab Initio Molecular Dynamics:  Sampling Methods and Thermostat Considerations

2004 ◽  
Vol 108 (12) ◽  
pp. 2167-2180 ◽  
Author(s):  
Evan Kelly ◽  
Michael Seth ◽  
Tom Ziegler
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio ◽  
Sampling Methods ◽  
Ab Initio Molecular Dynamics ◽  
Bimolecular Reactions ◽  
Energy Profiles ◽  
Free Energy Profiles

On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles

2002 ◽  
Vol 116 (11) ◽  
pp. 4389-4402 ◽  
Author(s):  
Lula Rosso ◽  
Peter Mináry ◽  
Zhongwei Zhu ◽  
Mark E. Tuckerman
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Energy Profiles ◽  
Free Energy Profiles

Energetics of nonpolar and polar compounds in cationic, anionic, and nonionic micelles studied by all-atom molecular dynamics simulation combined with a theory of solutions

2016 ◽  
Vol 18 (19) ◽  
pp. 13223-13231 ◽  
Author(s):  
Atsushi Date ◽  
Ryosuke Ishizuka ◽  
Nobuyuki Matubayasi
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Polar Compounds ◽  
Dynamics Simulation ◽  
Energy Profiles ◽  
Polar Solutes ◽  
Free Energy Profiles

Free-energy profiles of binding nonpolar and polar solutes in cationic, anionic, and nonionic micelles.

Unveiling conformational dynamics changes of H-Ras induced by mutations based on accelerated molecular dynamics

2020 ◽  
Vol 22 (37) ◽  
pp. 21238-21250
Author(s):  
Jianzhong Chen ◽  
Wei Wang ◽  
Laixue Pang ◽  
Weiliang Zhu
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Conformational Dynamics ◽  
Conformational Transformation ◽  
Accelerated Molecular Dynamics ◽  
Energy Profiles ◽  
Free Energy Profiles

The conformational transformation of two switches caused by mutations induces different free energy profiles of H-Ras.

Displacement of carbonates in Ca2UO2(CO3)3 by amidoxime-based ligands from free-energy simulations

2018 ◽  
Vol 47 (5) ◽  
pp. 1604-1613 ◽  
Author(s):  
Bo Li ◽  
Chad Priest ◽  
De-en Jiang
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Umbrella Sampling ◽  
Nacl Solution ◽  
Classical Molecular Dynamics ◽  
Energy Profiles ◽  
Energy Simulations ◽  
Dynamics Simulations ◽  
Free Energy Profiles

Classical molecular dynamics simulations coupled with umbrella sampling reveal the atomistic processes and free-energy profiles of the displacement of carbonate groups in the Ca2UO2(CO3)3 complex by amidoxime-based ligands in a 0.5 M NaCl solution.

The molecular mechanism of ligand unbinding from the human telomeric G-quadruplex by steered molecular dynamics and umbrella sampling simulations

2015 ◽  
Vol 17 (19) ◽  
pp. 12857-12869 ◽  
Author(s):  
Jia-Kai Zhou ◽  
Dah-Yen Yang ◽  
Sheh-Yi Sheu
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Mechanism ◽  
Steered Molecular Dynamics ◽  
Umbrella Sampling ◽  
Energy Profiles ◽  
G Quadruplex ◽  
Free Energy Profiles

The mechanical properties and kinetic pathways of the ligand BMVC unbinding from the G-quadruplex were investigated via the computation of free energy profiles.

MOLECULAR SIMULATION OF α-TOCOPHEROL PASSING ACROSS DPPC LIPID USING POTENTIAL OF MEAN FORCE AND ACCELERATED MOLECULAR DYNAMICS METHOD

2013 ◽  
Vol 12 (08) ◽  
pp. 1341011 ◽  
Author(s):  
FANCUI MENG
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Binding Free Energy ◽  
Computation Time ◽  
Potential Of Mean Force ◽  
Accelerated Molecular Dynamics ◽  
Energy Profiles ◽  
Lipid System ◽  
Dynamics Method ◽  
Free Energy Profiles

In this paper the process of α-tocopherol (TCP) passing across DPPC membrane was simulated using both the potential of mean force (PMF) and the accelerated molecular dynamics (aMD) methods, respectively. Energy properties, hydrogen bonds and orientation have been compared between these two methods and several conclusions have been obtained. The results indicate that TCP tends to stay at z = 1.2 nm of lipid bilayer. The binding free energy profiles of these two methods are alike. All these show that aMD could obtain comparable results as PMF method, while needs less computation time and resources. Therefore, aMD method could be used as an alternative method for prediction of transport properties of drug-lipid system.

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