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

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.
Equilibrium Conditions for a Particle01:23

Equilibrium Conditions for a Particle

When an object is in equilibrium, it is either at rest or moving with a constant velocity. There are two types of equilibrium: static and dynamic. Static equilibrium occurs when an object is at rest, while dynamic equilibrium occurs when an object is moving with a constant velocity. In both cases, there must be a balance of forces acting on the object.
To understand the concept of equilibrium, let us first consider the forces acting on an object. When different forces act on an object, they can...
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...

You might also read

Related Articles

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

Sort by
Same author

Machine Learning-Driven Drug Repurposing for KRAS G12C and KRAS G12D Inhibition.

ACS omega·2026
Same author

Dual-LAO for calculating fast and robust relative binding free energies of simple and complex transformations.

Communications chemistry·2026
Same author

Mechanism of Hydrolytic Instability of ZIF‑8 in Aqueous and Buffered Media: Implications on Drug Delivery Applications.

ACS omega·2026
Same author

Graph Neural Networks Model Based on Atomic Hybridization for Predicting Drug Targets.

Journal of chemical information and modeling·2026
Same author

Accurate Free Energy Calculation via Multiscale Simulations Driven by Hybrid Machine Learning and Molecular Mechanics Potentials.

Journal of chemical theory and computation·2025
Same author

Efficient and scalable electrostatics via spherical grids and treecode summation.

The Journal of chemical physics·2025

Related Experiment Video

Updated: Jun 12, 2026

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

11.8K

apoCHARMM: High-performance molecular dynamics simulations on GPUs for advanced simulation methods.

Samarjeet Prasad1, Felix Aviat1,2, James E Gonzales1,3

  • 1Laboratory of Computational Biology, National Heart, Lung, Blood Institute, National Institutes of Health, Bethesda, Maryland 30105, USA.

The Journal of Chemical Physics
|May 9, 2025
PubMed
Summary
This summary is machine-generated.

apoCHARMM is a new molecular dynamics (MD) engine that accelerates complex simulations on graphics processing units (GPUs). It enables advanced free energy calculations and lipid bilayer simulations with enhanced efficiency and performance.

More Related Videos

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

4.4K
Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function
05:57

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

300

Related Experiment Videos

Last Updated: Jun 12, 2026

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

11.8K
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

4.4K
Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function
05:57

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

300

Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Biophysics

Background:

  • Molecular dynamics (MD) simulations are crucial for understanding complex molecular systems.
  • Accelerating MD simulations requires efficient computational engines, particularly those leveraging graphics processing unit (GPU) architectures.
  • Existing MD engines may have limitations in handling multiple complex simulation setups or specific system types.

Purpose of the Study:

  • To introduce apoCHARMM, a high-performance MD engine optimized for GPU architectures.
  • To enable accelerated simulations of complex molecular systems, including advanced free energy calculations and lipid bilayer simulations.
  • To enhance the efficiency and capabilities of molecular simulations through novel computational strategies.

Main Methods:

  • Development of apoCHARMM using CUDA and modern C++ for GPU-exclusive computation.
  • Implementation of single-GPU support for multiple Hamiltonians, enabling advanced replica exchange and free energy methods.
  • Integration of full atomic virial tensor computation and support for orthorhombic P21 space groups for diverse ensemble simulations.

Main Results:

  • apoCHARMM demonstrates competitive or superior performance compared to existing GPU-based MD engines.
  • Efficient execution of multi-dimensional replica exchange and multi-state enveloping distribution sampling on a single GPU.
  • Successful simulation of constant-pH MD in explicit solvent and lipid bilayers with P21 space group support.

Conclusions:

  • apoCHARMM offers a versatile and high-performance solution for accelerating molecular dynamics simulations.
  • Its unique features facilitate efficient free energy calculations and the simulation of complex biological systems like lipid bilayers.
  • The GPU-exclusive design minimizes data transfer, maximizing computational efficiency for the molecular dynamics community.