Performing molecular dynamics simulations and computing hydration free energies on the B3LYP-D3 (BJ) potential energy surface with adaptive force matching: a …

D Zheng, F Wang - ACS Physical Chemistry Au, 2021 - ACS Publications
The potential energy surfaces at the B3LYP-D3 (BJ) level for eight solutes in dilute aqueous
solutions were mapped into simple pairwise additive force field expressions using the …

Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations

PV Klimovich, DL Mobley - Journal of Computer-Aided Molecular Design, 2010 - Springer
Molecular dynamics simulations in explicit solvent were applied to predict the hydration free
energies for 23 small organic molecules in blind SAMPL2 test. We found good agreement …

Hybrid alchemical free energy/machine-learning methodology for the computation of hydration free energies

J Scheen, W Wu, ASJS Mey, P Tosco… - Journal of Chemical …, 2020 - ACS Publications
A methodology that combines alchemical free energy calculations (FEP) with machine
learning (ML) has been developed to compute accurate absolute hydration free energies …

Assessing the accuracy of improved force‐matched water models derived from Ab initio molecular dynamics simulations

A Köster, T Spura, G Rutkai, J Kessler… - Journal of …, 2016 - Wiley Online Library
The accuracy of water models derived from ab initio molecular dynamics simulations by
means on an improved force‐matching scheme is assessed for various thermodynamic …

Optimizing solute–water van der Waals interactions to reproduce solvation free energies

PS Nerenberg, B Jo, C So, A Tripathy… - The Journal of …, 2012 - ACS Publications
An accurate representation of solute–water interactions is necessary for molecular dynamics
simulations of biomolecules that reside in aqueous environments. Modern force fields and …

Accurate prediction of the hydration free energies of 20 salts through adaptive force matching and the proper comparison with experimental references

J Li, F Wang - The Journal of Physical Chemistry B, 2017 - ACS Publications
Simple pairwise potentials for five alkali ions and four halide ions were developed by only
fitting to ab initio MP2 forces with the adaptive force matching (AFM) method. Without fitting …

Update to the general amber force field for small solutes with an emphasis on free energies of hydration

JPM Jambeck, AP Lyubartsev - The Journal of Physical Chemistry …, 2014 - ACS Publications
An approach to a straightforward reparametrization of the general AMBER force field (GAFF)
for small organic solutes and druglike compounds is presented. The parametrization is …

Infinite dilution activity coefficients as constraints for force field parametrization and method development

G Duarte Ramos Matos, G Calabro… - Journal of chemical …, 2019 - ACS Publications
Molecular simulations begin with an underlying energy model or force field and from this can
predict diverse physical properties. However, force fields were often developed with …

Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules

A Chakravorty, A Hussain, LF Cervantes… - Journal of Chemical …, 2024 - ACS Publications
Accurate force field parameters, potential energy functions, and receptor-ligand models are
essential for modeling the solvation and binding of drug-like molecules to a receptor. A large …

Predictions of hydration free energies from all-atom molecular dynamics simulations

DL Mobley, CI Bayly, MD Cooper… - The Journal of Physical …, 2009 - ACS Publications
Here, we computed the aqueous solvation (hydration) free energies of 52 small drug-like
molecules using an all-atom force field in explicit water. This differs from previous studies in …