Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Calculating Standard Free Energy Changes02:49

Calculating Standard Free Energy Changes

26.7K
The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
26.7K
Free Energy Changes for Nonstandard States03:25

Free Energy Changes for Nonstandard States

13.8K
The free energy change for a process taking place with reactants and products present under nonstandard conditions (pressures other than 1 bar; concentrations other than 1 M) is related to the standard free energy change according to this equation:
13.8K
Gibbs Free Energy02:39

Gibbs Free Energy

41.1K
One of the challenges of using the second law of thermodynamics to determine if a process is spontaneous is that it requires measurements of the entropy change for the system and the entropy change for the surroundings. An alternative approach involving a new thermodynamic property defined in terms of system properties only was introduced in the late nineteenth century by American mathematician Josiah Willard Gibbs. This new property is called the Gibbs free energy (G) (or simply the free...
41.1K
Gibbs Free Energy and Thermodynamic Favorability02:23

Gibbs Free Energy and Thermodynamic Favorability

9.0K
The spontaneity of a process depends upon the temperature of the system. Phase transitions, for example, will proceed spontaneously in one direction or the other depending upon the temperature of the substance in question. Likewise, some chemical reactions can also exhibit temperature-dependent spontaneities. To illustrate this concept, the equation relating free energy change to the enthalpy and entropy changes for the process is considered:
9.0K
Free Energy and Equilibrium00:55

Free Energy and Equilibrium

9.8K
The free energy change for a process may be viewed as a measure of its driving force. A negative value for ΔG represents a driving force for the process in the forward direction, while a positive value represents a driving force for the process in the reverse direction. When ΔG is zero, the forward and reverse driving forces are equal, and the process occurs in both directions at the same rate (the system is at equilibrium).
The reaction quotient, Q, is a convenient measure of the...
9.8K
Free Energy and Equilibrium02:56

Free Energy and Equilibrium

28.4K
The free energy change for a process may be viewed as a measure of its driving force. A negative value for ΔG represents a driving force for the process in the forward direction, while a positive value represents a driving force for the process in the reverse direction. When ΔGrxn is zero, the forward and reverse driving forces are equal, and the process occurs in both directions at the same rate (the system is at equilibrium).
Recall that Q is the numerical value of the mass action...
28.4K

You might also read

Related Articles

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

Sort by
Same author

Functional inactivation of MDR3 caused by a homozygous <i>ABCB4</i> missense variant leading to liver failure.

Frontiers in genetics·2026
Same author

LignAmb25: A comprehensive AMBER force field addressing lignin's structural and chemical diversity.

Biophysical journal·2026
Same author

Mechanisms of APOBEC3 Packaging into HIV-1.

Viruses·2026
Same author

Integrative approaches for the structure-based functional understanding of the ethylene response in plants.

The Plant journal : for cell and molecular biology·2026
Same author

Chat-Driven Computational (Bio)chemistry: Using LLM Agents to Accelerate Bio- and Chemoinformatics.

Journal of chemical information and modeling·2026
Same author

G521 is the gatekeeper and a key transmembrane domain contact residue of <i>Candida albicans</i> Cdr1.

mBio·2026

Related Experiment Video

Updated: Mar 29, 2026

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
15:05

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

9.5K

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.

Bill R Miller1, T Dwight McGee1, Jason M Swails1

  • 1Department of Chemistry, Quantum Theory Project, University of Florida , Gainesville, Florida 32611, United States.

Journal of Chemical Theory and Computation
|November 26, 2015
PubMed
Summary

MMPBSA.py streamlines molecular free energy calculations using various implicit solvation models. This Python program enhances efficiency for molecular dynamics and Monte Carlo simulations.

More Related Videos

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

8.8K
Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
05:56

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Published on: October 13, 2022

1.9K

Related Experiment Videos

Last Updated: Mar 29, 2026

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
15:05

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

9.5K
Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

8.8K
Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
05:56

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Published on: October 13, 2022

1.9K

Area of Science:

  • Computational chemistry
  • Molecular modeling

Background:

  • Molecular mechanics with Poisson-Boltzmann surface area (MM-PBSA) is a key method for calculating molecular free energies.
  • Accurate free energy calculations are crucial for understanding molecular interactions in solution.

Purpose of the Study:

  • To introduce MMPBSA.py, a Python program designed to simplify and accelerate MM-PBSA calculations.
  • To provide a flexible and user-friendly tool for end-state free energy computations.

Main Methods:

  • Utilizes ensembles from molecular dynamics (MD) or Monte Carlo (MC) simulations.
  • Incorporates multiple implicit solvation models: Poisson-Boltzmann, Generalized Born, and Reference Interaction Site Model.
  • Supports vibrational frequency analysis for solute entropy approximation and free energy decomposition/alanine scanning for interaction analysis.
  • Features a parallel implementation for enhanced computational speed.

Main Results:

  • MMPBSA.py offers an efficient and user-friendly approach to end-state free energy calculations.
  • The program supports diverse solvation models and advanced analysis techniques.
  • Parallel processing significantly reduces computation time.

Conclusions:

  • MMPBSA.py is a valuable and versatile tool for researchers performing molecular free energy calculations.
  • The program's flexibility and efficiency make it suitable for a wide range of computational chemistry applications.
  • Available as part of AmberTools under the GNU GPL.