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

Gibbs Free Energy02:39

Gibbs Free Energy

26.7K
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...
26.7K
Calculating Standard Free Energy Changes02:49

Calculating Standard Free Energy Changes

20.7K
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...
20.7K
Gibbs Free Energy and Thermodynamic Favorability02:23

Gibbs Free Energy and Thermodynamic Favorability

7.0K
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:
7.0K
Free Energy and Equilibrium00:55

Free Energy and Equilibrium

7.6K
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...
7.6K

You might also read

Related Articles

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

Sort by
Same author

Smoother Alchemical Transformations via Enveloping Distribution Sampling for Free-Energy Estimation.

Journal of chemical theory and computation·2026
Same author

Multiscale Neural Network Potential with Anisotropic Message Passing for the Fast and Accurate Simulation of Protein Dynamics and Enzymatic Reactions.

Journal of the American Chemical Society·2026
Same author

Balancing Data Quantity and Quality: Evaluating Curation Strategies for Bioactivity Prediction in Lead Optimization.

Journal of chemical information and modeling·2026
Same author

How well do classical and multiscale QM/MM molecular dynamics simulations capture stereoelectronic effects? A comparative study on atropisomerism.

The Journal of chemical physics·2026
Same author

Structures of ALG3/9/12 reveal the assembly logic of the N-glycan oligomannose core.

Nature chemical biology·2026
Same author

A Force Field Model for Actinyl Cations AnO<sub>2</sub><sup>2+</sup> and AnO<sub>2</sub><sup>+</sup> (An = U, Np, Pu) Comparable with the AMOEBA Polarizable Force Field.

Inorganic chemistry·2025

Related Experiment Video

Updated: Apr 30, 2026

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

8.2K

Replica-Exchange Enveloping Distribution Sampling: Calculation of Relative Free Energies in GROMOS.

Salomé R Rieder1, Benjamin Ries2, Candide Champion3

  • 1Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8092 Zurich. salome.rieder@phys.chem.ethz.ch.

Chimia
|December 9, 2023
PubMed
Summary

Molecular dynamics simulations aid drug design. The new replica-exchange enveloping distribution sampling (RE-EDS) method efficiently calculates free-energy differences for multiple molecules, showing good agreement with experimental data.

Keywords:
Computational chemistryFree energyRE-EDS

More Related Videos

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
06:37

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

Published on: September 17, 2021

4.5K
Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

2.3K

Related Experiment Videos

Last Updated: Apr 30, 2026

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

8.2K
Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
06:37

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

Published on: September 17, 2021

4.5K
Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

2.3K

Area of Science:

  • Computational Chemistry
  • Biophysics
  • Drug Discovery

Background:

  • Molecular dynamics (MD) simulations are crucial for studying biological systems.
  • Free-energy calculations using MD are vital for computer-aided drug design and material discovery.
  • Established methods like thermodynamic integration (TI) and Bennett's acceptance ratio (BAR) estimate free-energy differences.

Purpose of the Study:

  • Introduce the replica-exchange enveloping distribution sampling (RE-EDS) method.
  • Provide an overview of the RE-EDS computational pipeline.
  • Describe complementary tools: RestraintMaker and amber2gromos.

Main Methods:

  • Replica-exchange enveloping distribution sampling (RE-EDS) for estimating relative free-energy differences.
  • Utilizing a single simulation to analyze multiple molecules.
  • Application of RestraintMaker and amber2gromos tools.

Main Results:

  • RE-EDS enables efficient estimation of relative free-energy differences between multiple molecules.
  • Demonstrated good agreement between RE-EDS results and experimental values.
  • Validated RE-EDS against other established free-energy calculation methods.

Conclusions:

  • RE-EDS is a powerful and accurate method for free-energy calculations in computational chemistry.
  • The method shows promise for accelerating drug design and material discovery.
  • RE-EDS offers an attractive alternative to traditional free-energy calculation techniques.