Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Thermodynamic Potentials

Thermodynamic Potentials

Thermodynamic potentials are state functions that are extremely useful in analyzing a thermodynamic system. They have dimensions of energy. The four important thermodynamic potentials are internal energy, enthalpy, Helmholtz free energy, and Gibbs free energy. These thermodynamic potentials can be expressed using two of the following variables: pressure, volume, temperature, and entropy. These two variables are expressed as the rate of change of the thermodynamic potential with respect to other...

High-Resolution Mass Spectrometry (HRMS)

High-Resolution Mass Spectrometry (HRMS)

The resolution of a mass spectrometer depends on the efficiency of separating ions with different ion masses. The mass of an atom is approximated to the sum of the masses of protons and neutrons inside, considering the masses of protons and neutrons as equal. However, the masses of the proton (1.6726 × 10−24 g) and neutron (1.6749 × 10−24 g) are not truly equal. There is a minor error in the expression of atomic masses relative to the simplest atom of hydrogen. For...

Potential-Energy Criterion for Equilibrium

Potential-Energy Criterion for Equilibrium

Potential energy or potential function plays an essential role in determining the stability of a mechanical system. If a system is subjected to both gravitational and elastic forces, the potential function of the system can be expressed as the algebraic sum of gravitational and elastic potential energy. If the system is in equilibrium and is displaced by a small amount, then the work done on the system equals the negative of the change in the system's potential energy from the initial to the...

Molecular Orbital Theory I

Molecular Orbital Theory I

Overview of Molecular Orbital Theory

Molecular Orbital Theory II

Molecular Orbital Theory II

Molecular Orbital Energy Diagrams

Polymers: Defining Molecular Weight

Polymers: Defining Molecular Weight

Unlike small molecules with definite molecular weights, polymers are a mixture of individual polymer chains of varying lengths, each with a unique molecular weight. So, the molecular weight of a polymer is expressed as an average value based on the average size of the polymer chains. The two most common forms of averages used for polymers are the number average molecular weight and weight average molecular weight.
The number average molecular weight (Mn) is the summation of the number...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026

Same author

Machine Learning-Driven Drug Repurposing for KRAS G12C and KRAS G12D Inhibition.

ACS omega·2026

Same author

Context-dependent peptide recognition shapes tyrosine kinase substrate specificity beyond consensus motifs.

bioRxiv : the preprint server for biology·2026

Same author

A Hidden Binding Pocket in the β- ketoacyl-ACP Synthase FabB.

bioRxiv : the preprint server for biology·2026

Same author

Multiscale machine learning molecular mechanics for mechanism and stereoselectivity of Diels-Alderase catalysis.

Nature communications·2026

Same author

Comparison of Protein-Glycosaminoglycan Interactions in ff14sb/GLYCAM06j-1 and CHARMM36m Force Fields.

Journal of chemical information and modeling·2026

Search research articles

Related Experiment Video

Updated: Mar 24, 2026

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Published on: July 19, 2019

Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials.

Eric C Dybeck¹, Gerhard König², Bernard R Brooks²

¹Department of Chemical Engineering, University of Virginia , Charlottesville, Virginia 22904, United States.

Journal of Chemical Theory and Computation

|March 2, 2016

Summary

This summary is machine-generated.

We compared two reweighting methods for molecular solvation free energy calculations. Multistate Bennett acceptance ratio (MBAR) generally yields more accurate results than non-Boltzmann Bennett (NBB) when using QM/MM Hamiltonians.

More Related Videos

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

Related Experiment Videos

Last Updated: Mar 24, 2026

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Published on: July 19, 2019

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

Area of Science:

Computational Chemistry
Physical Chemistry
Molecular Modeling

Background:

Classical molecular mechanics (MM) is computationally efficient but less accurate for solvation free energy calculations.
Quantum mechanics/molecular mechanics (QM/MM) offers higher accuracy but is computationally expensive.
Reweighting techniques allow leveraging cheaper MM configurations for more expensive QM/MM calculations.

Purpose of the Study:

To compare the efficiency and accuracy of non-Boltzmann Bennett (NBB) and multistate Bennett acceptance ratio (MBAR) methods for reweighting MM configurations to QM/MM Hamiltonians.
To investigate optimal strategies for allocating computational resources in QM/MM reweighting.
To assess the performance of NBB and MBAR for solvation free energy calculations on the SAMPL4 dataset.

Main Methods:

Utilized Boltzmann reweighting with both NBB and MBAR to estimate QM/MM solvation free energy differences from MM configurations.
Employed B3LYP/6-31G* for solute and classical potentials for solvent (water).
Analyzed the variance of NBB and MBAR for identical datasets and evaluated performance on the SAMPL4 solvation dataset.

Main Results:

MBAR methods demonstrated smaller uncertainties compared to NBB methods for the ethane/methanol system.
Concentrating energy re-evaluations on MM states with high overlap to QM/MM states reduced variance.
MBAR showed marginally smaller variances than NBB on the SAMPL4 dataset, especially in systems with high sampling efficiency.
Switching from MM to QM/MM Hamiltonians reduced the Root Mean Square Deviation (RMSD) to experimental values by approximately 28% for SAMPL4 molecules.

Conclusions:

MBAR is generally more accurate than NBB for QM/MM reweighting of solvation free energies.
Efficient allocation of QM/MM calculations is crucial for minimizing variance and diagnosing sampling issues.
QM/MM calculations significantly improve the accuracy of solvation free energy predictions compared to MM alone.