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Related Concept Videos

Thermodynamic Potentials01:26

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...
Thermodynamic Processes01:25

Thermodynamic Processes

A thermodynamic process is a path through a sequence of states that takes a system from an initial state to a final state. In a cyclic process, the system returns to its initial state, so the changes in state properties and state functions (ΔT, Δp, ΔV, ΔU, ΔH) over one complete cycle are zero. However, heat and work transfers can still occur during the cycle, and the net heat and net work over the cycle need not be zero.A reversible process occurs when the system is infinitesimally close to...
Thermodynamic Systems01:06

Thermodynamic Systems

A thermodynamic system is a set of objects whose thermodynamic properties are of interest. The system is considered to be embedded in its surroundings or the environment. The system and its environment can exchange heat and do work on each other through a boundary that separates them. However, the immediate surroundings of the system interact with it directly and therefore have a much stronger influence on its behavior and properties.
Consider an example of  tea boiling in a kettle. The tea and...
Maxwell's Thermodynamic Relations01:23

Maxwell's Thermodynamic Relations

Maxwell's thermodynamic relations are very useful in solving problems in thermodynamics. Each of Maxwell's relations relates a partial differential between quantities that can be hard to measure experimentally to a partial differential between quantities that can be easily measured. These relations are a set of equations derivable from the symmetry of the second derivatives and the thermodynamic potentials.
All thermodynamic potentials are exact differentials. Therefore, their second-order...
Thermal Sigmatropic Reactions: Overview01:16

Thermal Sigmatropic Reactions: Overview

Sigmatropic rearrangements are a class of pericyclic reactions in which a σ bond migrates from one part of a π system to another. These are intramolecular rearrangements where the total number of σ and π bonds remain unchanged.
Sigmatropic shifts are classified based on an order term [i, j ], where i and j indicate the number of atoms across which each end of the σ bond migrates. Below are examples of a [3,3] sigmatropic shift in 1,5-hexadiene, referred to as...
Thermodynamics: Activity Coefficient01:24

Thermodynamics: Activity Coefficient

Activity is the measure of the effective concentration of the species in solution. It can be expressed as the product of the molar concentration of the species and its activity coefficient. The activity coefficient is a dimensionless quantity and depends on the total ionic strength of the solution.
The activity coefficient is a measure of the deviation from ideal behavior. When the ionic strength of the solution is minimal, the activity coefficient of an ionic species is close to unity, making...

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Updated: Jun 23, 2026

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

Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations.

César Augusto F de Oliveira1, Donald Hamelberg, J Andrew McCammon

  • 1Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365.

Journal of Chemical Theory and Computation
|May 23, 2009
PubMed
Summary
This summary is machine-generated.

This study presents an efficient accelerated Molecular Dynamics (MD) method to enhance free energy simulations. The approach improves accuracy by accelerating conformational transitions while preserving essential solvent interactions.

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Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

Area of Science:

  • Computational Chemistry
  • Molecular Dynamics Simulations

Background:

  • Free energy simulations are crucial for understanding molecular interactions in condensed phases.
  • Traditional methods often face challenges with accuracy and convergence, especially for complex systems.

Purpose of the Study:

  • To develop a straightforward and efficient approach to improve accuracy and convergence of free energy simulations.
  • To introduce a novel accelerated Molecular Dynamics (MD) method for enhancing molecular conformational transitions.

Main Methods:

  • Proposed a new accelerated MD approach that lowers energy barriers for conformational transitions.
  • Applied the method to propane-to-propane model systems for free energy calculations.
  • Enhanced sampling of internal degrees of freedom and incorporated solvent interactions.

Main Results:

  • Significantly improved accuracy and convergence of free energy simulations.
  • Accelerated MD approach efficiently samples low- and high-energy regions.
  • Maintained substantial populations near potential minima, preserving statistical integrity.

Conclusions:

  • The new accelerated MD approach enhances free energy simulations in condensed-phase systems.
  • Incorporating solvent interactions is critical for accurate and converged results.
  • The method effectively recovers ensemble averages in thermodynamic integration calculations.