scholarly journals Exploring the free energy surface using ab initio molecular dynamics

2016 ◽  
Vol 144 (16) ◽  
pp. 164101 ◽  
Author(s):  
Amit Samanta ◽  
Miguel A. Morales ◽  
Eric Schwegler
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio ◽  
Energy Surface ◽  
Ab Initio Molecular Dynamics ◽  
Free Energy Surface

scholarly journals An approach to calculate the free energy changes of surface reactions using free energy decomposition on ab initio brute-force molecular dynamics trajectories

2020 ◽  
Vol 22 (37) ◽  
pp. 21340-21349
Author(s):  
Jiayan Xu ◽  
Hao Huang ◽  
P. Hu
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio ◽  
Energy Surface ◽  
Brute Force ◽  
Energy Decomposition ◽  
Free Energy Surface ◽  
Free Energy Decomposition ◽  
Kinetics Of ◽  
Kinetics Of Catalytic Reactions

To understand the mechanisms and kinetics of catalytic reactions in heterogeneous catalysis, ab initio molecular dynamics is one of the powerful methods used to explore the free energy surface (FES) of surface elementary steps.

scholarly journals Water Dipole and Quadrupole Moment Contributions to the Ion Hydration Free Energy by the Deep Neural Network Trained with Ab Initio Molecular Dynamics Data

2020 ◽  
Author(s):  
YU SHI ◽  
Carrie C. Doyle ◽  
Thomas L. Beck
Keyword(s):  
Neural Network ◽  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio ◽  
Deep Neural Network ◽  
Ab Initio Molecular Dynamics ◽  
Quadrupole Moments ◽  
Hydration Free Energy ◽  
Ion Hydration ◽  
Water Dipole

<div>We report a calculation scheme on water molecular dipole and quadrupole moments in the liquid phase through a Deep Neural Network (DNN) model. Employing the the Maximally Localized Wannier Functions (MLWF) for the valence electrons, we obtain the water moments through a post-process on trajectories from \textit{ab-initio} molecular dynamics (AIMD) simulations at the density functional theory (DFT) level. In the framework of the deep potential molecular dynamics (DPMD), we develop a scheme to train a DNN with the AIMD moments data. Applying the model, we calculate the contributions from water dipole and quadrupole moments to the electrostatic potential at the center of a cavity of radius 4.1 \AA\ as -3.87 V, referenced to the average potential in the bulk-like liquid region.</div><div>To unravel the ion-independent water effective local potential contribution to the ion hydration free energy, we estimate the 3rd cumulant term as -0.22 V from simulations totally over 6 ns, a time-scale inaccessible for AIMD calculations. </div>

ACTION-DERIVED AB INITIO MOLECULAR DYNAMICS

2009 ◽  
Vol 01 (03) ◽  
pp. 469-482 ◽  
Author(s):  
S. JUN ◽  
S. PENDURTI ◽  
I.-H. LEE ◽  
S. Y. KIM ◽  
H. S. PARK ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Energy Surface ◽  
Atomic System ◽  
Minimum Energy ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Least Action Principle ◽  
Least Action ◽  
Long Time

Action-derived molecular dynamics (ADMD) is a numerical method to search for minimum-energy dynamic pathways on the potential-energy surface of an atomic system. The method is based on Hamilton's least-action principle and has been developed for problems of activated processes, rare events, and long-time simulations. In this paper, ADMD is further extended to incorporate ab initio total-energy calculations, which enables the detailed electronic analysis of transition states as well as the exploration of energy landscapes. Three numerical examples are solved to demonstrate the capability of this action-derived ab initio molecular dynamics (MD). The proposed approach is expected to circumvent the severe time-scale limitation of conventional ab intio MD simulations.

scholarly journals Ultrafast proton transport in water-methanol mixtures

2019 ◽  
Vol 205 ◽  
pp. 09004
Author(s):  
Maria Ekimova ◽  
Felix Hoffmann ◽  
Gul Bekcioglu-Neff ◽  
Aidan Rafferty ◽  
Erik T. J. Nibbering ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Proton Transport ◽  
Ab Initio Molecular Dynamics ◽  
Transport Pathway ◽  
Pump Probe ◽  
Dynamics Simulations

Femtosecond UV/IR pump-probe experiments and ab initio molecular dynamics simulations of 7-hydroxyquinoline in water-methanol mixtures demonstrate an unexpectedly dominant OH-/CH3O- transport pathway but consistent with a solvent-dependent photoacidity free energy-reactivity correlation behaviour.

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