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

Solvents

Solvents

A solvent is a substance, most often a liquid, that can dissolve other substances. Here, the substance being dissolved is called a solute. When a solvent and a solute combine, they form a solution - a homogenous mixture of both the solvent and the solute. Water is a universal biological solvent. Its polar structure allows it to dissolve many other polar compounds. The ability of water to dissolve is governed by a balance between water molecules binding to each other and binding to the solute.
A...

Molecular Comparison of Gases, Liquids, and Solids

Molecular Comparison of Gases, Liquids, and Solids

Particles in a solid are tightly packed together (fixed shape) and often arranged in a regular pattern; in a liquid, they are close together with no regular arrangement (no fixed shape); in a gas, they are far apart with no regular arrangement (no fixed shape). Particles in a solid vibrate about fixed positions (cannot flow) and do not generally move in relation to one another; in a liquid, they move past each other (can flow) but remain in essentially constant contact; in a gas, they move...

Chemical Shift: Internal References and Solvent Effects

Chemical Shift: Internal References and Solvent Effects

In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
The internal reference compound generally used in NMR spectroscopy is tetramethylsilane (TMS). TMS is preferred because it is chemically inert, soluble in NMR solvents, and easily removable. Also, the highly shielded methyl protons in TMS yield an intense...

Accelerating Fluids

Accelerating Fluids

When a fluid is in constant acceleration, the pressure and buoyant force equations are modified. Suppose a beaker is placed in an elevator accelerating upward with a constant acceleration, a. In the beaker, assume there is a thin cylinder of height h with an infinitesimal cross-sectional area, ΔS.
The motion of the liquid within this infinitesimal cylinder is considered to obtain the pressure difference. Three vertical forces act on this liquid:

Chemical and Solubility Equilibria

Chemical and Solubility Equilibria

The free energy change associated with dissolving a solute in a liter of solvent is called the free energy of a solution, ΔGsolution. The overall ΔGsolution is expressed as the balance of ΔGinteraction against the always-favorable free-energy of mixing, ΔGmixing. Solution formation is favorable if ΔGsolution is less than zero, whereas it is unfavorable if ΔGsolution is greater than zero. In short, for a solution to form and complete dissolution to take place, the Gibbs energy change must be...

You might also read

Related Articles

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

Sort by

Same author

A Structural Ensemble of Hen Egg-White Lysozyme in Aqueous Solution Based on 2043 NMR NOE, <sup>3</sup><i>J</i>-Coupling and <i>S</i><sup>2</sup> Order-Parameter Data.

The journal of physical chemistry. B·2025

Same author

Use of Measured Residual Dipolar Couplings to Calculate Residual Dipolar Couplings for a Protein Structure: A Case Study Using Hen Egg-White Lysozyme.

Journal of chemical information and modeling·2025

Same author

Correction to "Molecular Structure Refinement of a β-Heptapeptide Based on Residual Dipolar Couplings: The Challenge of Extracting Structural Information from Measured RDCs".

The journal of physical chemistry. B·2025

Same author

Correction to "Molecular Structure Refinement Based on Residual Dipolar Couplings: A Comparison of the Molecular Rotational-Sampling Method with the Alignment-Tensor Approach".

Journal of chemical information and modeling·2025

Same author

Molecular Structure Refinement of a ß-Heptapeptide Based on Residual Dipolar Couplings: The Challenge of Extracting Structural Information from Measured RDCs.

The journal of physical chemistry. B·2025

Same author

Methods for Classical-Mechanical Molecular Simulation in Chemistry: Achievements, Limitations, Perspectives.

Journal of chemical information and modeling·2024

Search research articles

Related Experiment Video

Updated: Jun 16, 2026

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Published on: December 18, 2014

A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software.

Nathan Schmid¹, Mathias Bötschi, Wilfred F van Gunsteren

¹Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, Zürich 8093, Switzerland.

Journal of Computational Chemistry

|February 4, 2010

Summary

This summary is machine-generated.

Graphics processing units (GPUs) accelerate molecular dynamics simulations by enabling faster solvent-solvent interaction evaluation. This GPU implementation maintains accuracy, speeding up simulations by 6-9 times.

More Related Videos

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Published on: September 1, 2023

Related Experiment Videos

Last Updated: Jun 16, 2026

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Published on: December 18, 2014

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Published on: September 1, 2023

Area of Science:

Computational chemistry
High-performance computing

Background:

Graphics Processing Units (GPUs) are increasingly utilized in high-performance computing.
Molecular dynamics (MD) simulations require significant computational resources, particularly for evaluating solvent-solvent interactions.

Purpose of the Study:

To present an optimized acceleration engine for solvent-solvent interaction evaluation in MD simulations using GPUs.
To investigate the accuracy of a single-precision GPU implementation for these calculations.

Main Methods:

Implementation of a GPU-based acceleration engine for GROMOS software.
Careful algorithm optimization for GPU architecture.
Rigorous accuracy assessment of single-precision GPU results compared to double-precision CPU.

Main Results:

Achieved speed-ups of up to 54x (single-precision GPU vs. double-precision CPU).
Confirmed that single-precision GPU implementation does not compromise structural, thermodynamic, or dynamic quantities.
Demonstrated practical speed-ups of 6-9x for users of the GROMOS software.

Conclusions:

The GPU acceleration engine effectively speeds up solvent-solvent interaction evaluation in MD simulations.
The implementation offers a significant performance improvement without sacrificing simulation accuracy.
Enables wider adoption of GPU computing for biomolecular simulations within the GROMOS ecosystem.