Exciton transfer free energy from Car–Parrinello molecular dynamics

2020 ◽  
Vol 22 (19) ◽  
pp. 10526-10535
Author(s):  
Christian Schwermann ◽  
Nikos L. Doltsinis
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio ◽  
Molecular Orbitals ◽  
Free Energies ◽  
Electron Hole ◽  
Transfer Free Energy ◽  
Transfer Processes ◽  
Exciton Transfer ◽  
Electron Hole Pair

Free energies profiles for exciton transfer processes are calculated within ab initio molecular dynamics by applying restraining potentials to the Wannier centres of molecular orbitals corresponding to an electron-hole pair.

scholarly journals Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision and Reproducibility

2021 ◽  
Author(s):  
Alexander Wade ◽  
Agastya Bhati ◽  
Shunzhou Wan ◽  
Peter Coveney
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Binding Free Energy ◽  
Thermodynamic Integration ◽  
Free Energy Perturbation ◽  
Free Energies ◽  
Ensemble Averaging ◽  
Relative Binding ◽  
Energy Perturbation ◽  
Binding Free Energies

The binding free energy between a ligand and its target protein is an essential quantity to know at all stages of the drug discovery pipeline. Assessing this value computationally can offer insight into where efforts should be focused in the pursuit of effective therapeutics to treat myriad diseases. In this work we examine the computation of alchemical relative binding free energies with an eye to assessing reproducibility across popular molecular dynamics packages and free energy estimators. The focus of this work is on 54 ligand transformations from a diverse set of protein targets: MCL1, PTP1B, TYK2, CDK2 and thrombin. These targets are studied with three popular molecular dynamics packages: OpenMM, NAMD2 and NAMD3. Trajectories collected with these packages are used to compare relative binding free energies calculated with thermodynamic integration and free energy perturbation methods. The resulting binding free energies show good agreement between molecular dynamics packages with an average mean unsigned error between packages of 0.5 $kcal/mol$ The correlation between packages is very good with the lowest Spearman's, Pearson's and Kendall's tau correlation coefficient between two packages being 0.91, 0.89 and 0.74 respectively. Agreement between thermodynamic integration and free energy perturbation is shown to be very good when using ensemble averaging.

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>

scholarly journals Improved Sampling in Ab Initio Free Energy Calculations of Biomolecules at Solid–Liquid Interfaces: Tight-Binding Assessment of Charged Amino Acids on TiO2 Anatase (101)

Computation ◽  
2020 ◽  
Vol 8 (1) ◽  
pp. 12 ◽  
Author(s):  
Lorenzo Agosta ◽  
Erik G. Brandt ◽  
Alexander Lyubartsev
Keyword(s):  
Amino Acids ◽  
Free Energy ◽  
Ab Initio ◽  
Tight Binding ◽  
Free Energy Calculations ◽  
Free Energies ◽  
Ab Initio Simulations ◽  
Adsorption Free Energy ◽  
Charged Amino Acids ◽  
Solid Liquid

Atomistic simulations can complement the scarce experimental data on free energies of molecules at bio-inorganic interfaces. In molecular simulations, adsorption free energy landscapes are efficiently explored with advanced sampling methods, but classical dynamics is unable to capture charge transfer and polarization at the solid–liquid interface. Ab initio simulations do not suffer from this flaw, but only at the expense of an overwhelming computational cost. Here, we introduce a protocol for adsorption free energy calculations that improves sampling on the timescales relevant to ab initio simulations. As a case study, we calculate adsorption free energies of the charged amino acids Lysine and Aspartate on the fully hydrated anatase (101) TiO2 surface using tight-binding forces. We find that the first-principle description of the system significantly contributes to the adsorption free energies, which is overlooked by calculations with previous methods.

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