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

Molecular Models02:00

Molecular Models

41.8K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
41.8K
Molecular Comparison of Gases, Liquids, and Solids02:26

Molecular Comparison of Gases, Liquids, and Solids

46.6K
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...
46.6K
Distribution of Molecular Speeds01:27

Distribution of Molecular Speeds

4.3K
The motion of molecules in a gas is random in magnitude and direction for individual molecules, but a gas of many molecules has a predictable distribution of molecular speeds. This predictable distribution of molecular speeds is known as the Maxwell-Boltzmann distribution. The distribution of molecular speeds in liquids is comparable to that of gases but not identical and can help to understand the phenomenon of the boiling and vapor pressure of a liquid. Consider that a molecule requires a...
4.3K
Molecular Shapes01:18

Molecular Shapes

59.3K
Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...
59.3K
Predicting Molecular Geometry02:27

Predicting Molecular Geometry

37.7K
VSEPR Theory for Determination of Electron Pair Geometries
37.7K
Molecular Orbital Theory I02:35

Molecular Orbital Theory I

35.9K
Overview of Molecular Orbital Theory
35.9K

You might also read

Related Articles

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

Sort by
Same author

Comparing Enhanced Sampling Methods in Exploring the Conformational Space of β-Catenin<sub>17-48</sub>.

The journal of physical chemistry. B·2026
Same author

Extracellular 70 kDa heat shock protein in blood plasma binds insulin and modulates glycaemic control in vivo.

Cell stress & chaperones·2026
Same author

eRMSF: A Python Package for Ensemble-Based RMSF Analysis of Biomolecular Systems.

Journal of chemical information and modeling·2025
Same author

ParametrizANI: Fast and Accessible Dihedral Parametrization for Small Molecules.

Journal of chemical information and modeling·2025
Same author

Structural Modeling of NTPDase-Substrate Complexes Preserving Catalytic Experimental Features.

ACS omega·2025
Same author

Running Gaussian-accelerated Molecular Dynamics Simulations in NAMD [Article v1.0].

Living journal of computational molecular science·2025
Same journal

QSAR in the Browser: An Interactive Cheminformatics Web Application.

Journal of chemical information and modeling·2026
Same journal

FoldDoF: Utilizing the Primary Degrees of Freedom of Protein Backbone for Geometric Modeling and Generation.

Journal of chemical information and modeling·2026
Same journal

Derisking Affinity Optimization for Macrocycles and Cyclic Peptides: High-Precision Free Energy Simulations across Five Diverse Targets.

Journal of chemical information and modeling·2026
Same journal

An End-User Audit of Reproducibility, Data Leakage, and Overfitting of the Top-Ranked ADMET Prediction Models in TDC Leaderboards.

Journal of chemical information and modeling·2026
Same journal

PFASGroups: An Open-Source Framework for Automated Identification, Structural Classification, and Prioritization of Per- and Polyfluoroalkyl Substances.

Journal of chemical information and modeling·2026
Same journal

DeepKbhb: Context-Aware Prediction of Human Lysine β-Hydroxybutyrylation Sites.

Journal of chemical information and modeling·2026
See all related articles

Related Experiment Video

Updated: Oct 18, 2025

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis
11:29

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

Published on: December 18, 2014

12.1K

Making it Rain: Cloud-Based Molecular Simulations for Everyone.

Pablo R Arantes1, Marcelo D Polêto2, Conrado Pedebos3

  • 1Department of Bioengineering, University of California, Riverside, California 92521, United States.

Journal of Chemical Information and Modeling
|October 1, 2021
PubMed
Summary
This summary is machine-generated.

This work introduces an accessible platform for molecular dynamics (MD) simulations using OpenMM on Google Colab. It supports education and enables microsecond-scale simulations for researchers with limited resources.

More Related Videos

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

1.5K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.3K

Related Experiment Videos

Last Updated: Oct 18, 2025

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis
11:29

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

Published on: December 18, 2014

12.1K
Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

1.5K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.3K

Area of Science:

  • Computational Chemistry
  • Biophysics
  • Materials Science

Background:

  • Molecular dynamics (MD) simulations are crucial for understanding molecular behavior but often require significant computational resources.
  • Existing MD simulation platforms can have steep learning curves and high hardware costs, limiting accessibility.

Discussion:

  • This study introduces a user-friendly front-end for OpenMM, leveraging Google Colab for accessible cloud-based molecular dynamics simulations.
  • The platform is designed for educational purposes, offering a hands-on approach to learning MD simulation techniques.
  • It demonstrates the feasibility of performing microsecond-timescale MD simulations, even for research groups with limited financial resources.

Key Insights:

  • The developed front-end simplifies the execution of complex MD simulations.
  • Google Colab provides a viable and cost-effective cloud computing solution for academic research.
  • Microsecond-timescale simulations are achievable, broadening the scope of accessible computational research.

Outlook:

  • This initiative aims to democratize MD simulations, making them more accessible for teaching and research globally.
  • Further development could include integration with more analysis tools and support for larger biomolecular systems.
  • The platform has the potential to foster wider adoption of computational methods in scientific education and discovery.