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

Recrystallization: Solid–Solution Equilibria01:10

Recrystallization: Solid–Solution Equilibria

1.6K
Recrystallization is a purification technique used to separate impurities from solid compounds. In this technique, no chemical reactions occur. Instead, it exploits physical properties only, specifically, the solubility differences between the desired compound and impurities, either at a single temperature or at different temperatures, and under other selected conditions. The solid-solution equilibrium (solubility equilibrium) of each component in the solution represents a binary phase...
1.6K
Solution Equilibrium and Saturation01:59

Solution Equilibrium and Saturation

20.5K
Imagine adding a small amount of sugar to a glass of water, stirring until all the sugar has dissolved, and then adding a bit more. You can repeat this process until the sugar concentration of the solution reaches its natural limit, a limit determined primarily by the relative strengths of the solute-solute, solute-solvent, and solvent-solvent attractive forces. You can be certain that you have reached this limit because, no matter how long you stir the solution, undissolved sugar remains. The...
20.5K
Precipitation Processes01:12

Precipitation Processes

1.8K
The experimental conditions in a gravimetric analysis should be optimized to maximize the particle size and purity of the obtained precipitate. Ideally, the concentration of the precipitating reagent should be low with effective stirring to maintain low relative supersaturation for the growth of large crystals. In homogeneous precipitation, the precipitant is slowly generated by a chemical reaction in the solution to avoid local reagent excesses. For example, urea decomposes gradually to...
1.8K
Expressing Solution Concentration02:48

Expressing Solution Concentration

63.7K
A solute is a component of a solution that is typically present at a much lower concentration than the solvent. Solute concentrations are often described with qualitative terms such as dilute (of relatively low concentration) and concentrated (of relatively high concentration).
Concentrations may be quantitatively assessed using a wide variety of measurement units, each convenient for particular applications. Molarity (M) is a useful concentration unit for many applications in chemistry.
63.7K
Precipitation of Ions03:11

Precipitation of Ions

28.8K
Predicting Precipitation
The equation that describes the equilibrium between solid calcium carbonate and its solvated ions is:
28.8K

You might also read

Related Articles

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

Sort by
Same author

Minimal Collective Variables for Conformational Transitions in Steered and Temperature-Accelerated MD Simulations: A T4 Lysozyme Case Study.

The journal of physical chemistry. B·2025
Same author

Optimization of a Piperidine CD4-Mimetic Scaffold Sensitizing HIV-1 Infected Cells to Antibody-Dependent Cellular Cytotoxicity.

ACS medicinal chemistry letters·2024
Same author

Structure and energetics guide dynamic behaviour in a T = 3 icosahedral virus capsid.

Biophysical chemistry·2023
Same author

Pharmacophore Variants of the Macrocyclic Peptide Triazole Inactivator of HIV-1 Env.

Research square·2023
Same author

Molecular Dynamics Simulations of Ion Permeation in Human Voltage-Gated Sodium Channels.

Journal of chemical theory and computation·2023
Same author

Structural and Functional Characterization of Indane-Core CD4-Mimetic Compounds Substituted with Heterocyclic Amines.

ACS medicinal chemistry letters·2023

Related Experiment Video

Updated: Nov 2, 2025

Reliable Mechanochemistry: Protocols for Reproducible Outcomes of Neat and Liquid Assisted Ball-mill Grinding Experiments
13:05

Reliable Mechanochemistry: Protocols for Reproducible Outcomes of Neat and Liquid Assisted Ball-mill Grinding Experiments

Published on: January 23, 2018

10.8K

Optimizing String Method's Reproducibility Using Generalized Solute Tempering Replica Exchange.

Gourav Shrivastav1, Cameron F Abrams1

  • 1Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States.

The Journal of Physical Chemistry. B
|June 10, 2021
PubMed
Summary

Generalized replica exchange solute tempering (gREST) enhances molecular simulations for accurate free energy calculations. Combining gREST with temperature-accelerated MD and the string method improves sampling and pathway characterization for complex systems.

More Related Videos

Author Spotlight: Accelerating Discovery in Microporous Material Chemistry
07:20

Author Spotlight: Accelerating Discovery in Microporous Material Chemistry

Published on: October 6, 2023

4.0K
Methods of Ex Situ and In Situ Investigations of Structural Transformations: The Case of Crystallization of Metallic Glasses
08:55

Methods of Ex Situ and In Situ Investigations of Structural Transformations: The Case of Crystallization of Metallic Glasses

Published on: June 7, 2018

8.7K

Related Experiment Videos

Last Updated: Nov 2, 2025

Reliable Mechanochemistry: Protocols for Reproducible Outcomes of Neat and Liquid Assisted Ball-mill Grinding Experiments
13:05

Reliable Mechanochemistry: Protocols for Reproducible Outcomes of Neat and Liquid Assisted Ball-mill Grinding Experiments

Published on: January 23, 2018

10.8K
Author Spotlight: Accelerating Discovery in Microporous Material Chemistry
07:20

Author Spotlight: Accelerating Discovery in Microporous Material Chemistry

Published on: October 6, 2023

4.0K
Methods of Ex Situ and In Situ Investigations of Structural Transformations: The Case of Crystallization of Metallic Glasses
08:55

Methods of Ex Situ and In Situ Investigations of Structural Transformations: The Case of Crystallization of Metallic Glasses

Published on: June 7, 2018

8.7K

Area of Science:

  • Computational chemistry
  • Molecular dynamics simulations
  • Biophysics

Background:

  • Accurate free energy calculations in molecular simulations are challenging due to hidden variables and sampling limitations.
  • High-dimensional free energy landscapes require computationally expensive methods for efficient exploration.
  • Existing methods like temperature-accelerated MD (TAMD) and the string method (SM) can be limited by sampling restrictions.

Purpose of the Study:

  • To enhance sampling and improve the accuracy and reproducibility of free energy predictions in molecular simulations.
  • To investigate the efficacy of combining generalized replica exchange solute tempering (gREST) with TAMD and SM.
  • To assess the computational cost-effectiveness of gREST-enabled methods for exploring complex systems.

Main Methods:

  • Implementation of gREST-enabled TAMD and SM.
  • Utilizing two distinct collective variable representations for the pentapeptide neurotransmitter met-enkephalin.
  • Comparing the performance of gREST-enabled methods against standalone TAMD and SM.

Main Results:

  • gREST-enabled TAMD and SM demonstrated more accurate and reproducible free energy predictions compared to TAMD and SM alone.
  • The combined methods effectively addressed sampling limitations posed by hidden variables.
  • gREST offered enhanced sampling at a moderate computational cost relative to other replica-exchange methods.

Conclusions:

  • gREST-enabled TAMD and SM provide a more robust approach for free energy calculations in complex molecular systems.
  • The gREST-enabled string method is a computationally attractive tool for characterizing free energy minima and pathways.
  • This approach offers a promising strategy for a wide range of systems requiring accurate free energy landscape analysis.