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

Molecular Models

Molecular Models

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.

Multimachine Stability

Multimachine Stability

Multimachine stability analysis is crucial for understanding the dynamics and stability of power systems with multiple synchronous machines. The objective is to solve the swing equations for a network of M machines connected to an N-bus power system.
In analyzing the system, the nodal equations represent the relationship between bus voltages, machine voltages, and machine currents. The nodal equation is given by:

You might also read

Related Articles

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

Sort by

Same author

<i>seekrflow</i>: Towards an End-to-End Automated Simulation Pipeline with Machine-Learned Force Fields for Accelerated Drug-Target Kinetic and Thermodynamic Predictions.

Journal of chemical theory and computation·2026

Same author

Condensate-Like Organization in Respiratory Aerosols Modulates the Dynamics of an Airborne Virus.

bioRxiv : the preprint server for biology·2026

Same author

D614G reshapes allosteric networks and opening mechanisms of SARS-CoV-2 spikes.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

Advancing Reproducibility and Open Data in Theoretical and Computational Chemistry.

Journal of chemical theory and computation·2026

Same author

Detection of gas bubbles and local voids in molecular simulations using burbuja.

Protein science : a publication of the Protein Society·2026

Same author

N-Glycans modulate tilting of HIV-1 envelope glycoprotein.

Nature communications·2026

Search research articles

Related Experiment Video

Updated: Sep 6, 2025

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

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

Published on: April 12, 2019

SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine.

Lane W Votapka¹, Andrew M Stokely¹, Anupam A Ojha¹

¹University of California, San Diego, 9500 Gilman Dr., La Jolla, California 92093, United States.

Journal of Chemical Information and Modeling

|June 27, 2022

Summary

SEEKR2, a new computational tool, accurately estimates molecular binding kinetics faster than previous versions. It enhances usability and speed for molecular process simulations.

More Related Videos

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

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

Published on: September 17, 2021

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Published on: July 19, 2019

Related Experiment Videos

Last Updated: Sep 6, 2025

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

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

Published on: April 12, 2019

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

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

Published on: September 17, 2021

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Published on: July 19, 2019

Area of Science:

Computational Chemistry
Molecular Dynamics
Biophysics

Background:

Estimating molecular kinetics and thermodynamics is crucial for understanding biological processes.
Previous SEEKR versions enabled computational estimation of these properties.
Advancements in computational power and algorithms necessitate updated simulation tools.

Purpose of the Study:

To introduce SEEKR2 (simulation-enabled estimation of kinetic rates version 2), an improved software for calculating molecular process kinetics and thermodynamics.
To enhance the speed, capabilities, and usability of the SEEKR software family.
To enable accurate prediction of ligand-receptor binding kinetics.

Main Methods:

Utilized multiscale simulation methods.
Integrated the OpenMM simulation engine alongside NAMD.
Upgraded the Brownian dynamics component to Browndye 2.
Implemented hydrogen mass repartitioning to reduce computational cost.

Main Results:

SEEKR2 achieves equivalent or improved results compared to earlier SEEKR versions.
Demonstrated significant increases in computational speed and overall capabilities.
Showed minimal to no loss of accuracy in predicted kinetics with hydrogen mass repartitioning.

Conclusions:

SEEKR2 offers a faster, more capable, and user-friendly platform for molecular kinetics and thermodynamics estimation.
The software is extensible for future method development.
Hydrogen mass repartitioning is an effective strategy for reducing computational expense without compromising accuracy.