Machine-learning-assisted free energy simulation of solution-phase and enzyme reactions
Despite recent advances in the development of machine learning potentials (MLPs) for
biomolecular simulations, there has been limited effort on develo** stable and accurate …
biomolecular simulations, there has been limited effort on develo** stable and accurate …
Perspective: Reference-Potential Methods for the Study of Thermodynamic Properties in Chemical Processes: Theory, Applications, and Pitfalls
In silico investigations of enzymatic reactions and chemical reactions in condensed phases
often suffer from formidable computational costs due to a large number of degrees of …
often suffer from formidable computational costs due to a large number of degrees of …
Multireference generalization of the weighted thermodynamic perturbation method
We describe the generalized weighted thermodynamic perturbation (gwTP) method for
estimating the free energy surface of an expensive “high-level” potential energy function …
estimating the free energy surface of an expensive “high-level” potential energy function …
PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics
PyDFT-QMMM is a Python-based package for performing hybrid quantum
mechanics/molecular mechanics (QM/MM) simulations at the density functional level of …
mechanics/molecular mechanics (QM/MM) simulations at the density functional level of …
Factors that determine the variation of equilibrium and kinetic properties of QM/MM enzyme simulations: QM region, conformation, and boundary condition
D Demapan, J Kussmann… - Journal of chemical …, 2022 - ACS Publications
To analyze the impact of various technical details on the results of quantum mechanical
(QM)/molecular mechanical (MM) enzyme simulations, including the QM region size …
(QM)/molecular mechanical (MM) enzyme simulations, including the QM region size …
Tracking the delocalized proton in concerted proton transfer in bulk water
A solvated proton in water is often characterized as a charge or structural defect, and it is
important to track its evolution on-the-fly in certain dynamics simulations. Previously, we …
important to track its evolution on-the-fly in certain dynamics simulations. Previously, we …
Exploring Routes to Enhance the Calculation of Free Energy Differences via Non-Equilibrium Work SQM/MM Switching Simulations Using Hybrid Charge …
Non-equilibrium work switching simulations and Jarzynski's equation are a reliable method
for computing free energy differences, Δ A low→ high, between two levels of theory, such as …
for computing free energy differences, Δ A low→ high, between two levels of theory, such as …
Accelerating Ab Initio Quantum Mechanical and Molecular Mechanical (QM/MM) Molecular Dynamics Simulations with Multiple Time Step Integration and a …
Molecular dynamics (MD) simulations employing ab initio quantum mechanical and
molecular mechanical (ai-QM/MM) potentials are considered to be the state of the art, but the …
molecular mechanical (ai-QM/MM) potentials are considered to be the state of the art, but the …
Quantum vibrational spectroscopy of explicitly solvated thymidine in semiclassical approximation
In this paper, we demonstrate the possibility to perform spectroscopy simulations of solvated
biological species taking into consideration quantum effects and explicit solvation. We …
biological species taking into consideration quantum effects and explicit solvation. We …
BAR‐Based Multi‐Dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscapes: Varying the QM Region
Z Sun, Z Liu - Advanced Theory and Simulations, 2021 - Wiley Online Library
The indirect free energy simulation at quantum mechanics (QM)/molecular mechanics (MM)
levels provides a feasible alternative to direct QM/MM simulations. The main idea under the …
levels provides a feasible alternative to direct QM/MM simulations. The main idea under the …