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

Coordination Number and Geometry02:57

Coordination Number and Geometry

16.9K
For transition metal complexes, the coordination number determines the geometry around the central metal ion. Table 1 compares coordination numbers to molecular geometry. The most common structures of the complexes in coordination compounds are octahedral, tetrahedral, and square planar.
16.9K
Statically Indeterminate Problem Solving01:16

Statically Indeterminate Problem Solving

523
Statically indeterminate problems are those where statics alone can not determine the internal forces or reactions. Consider a structure comprising two cylindrical rods made of steel and brass. These rods are joined at point B and restrained by rigid supports at points A and C. Now, the reactions at points A and C and the deflection at point B are to be determined. This rod structure is classified as statically indeterminate as the structure has more supports than are necessary for maintaining...
523
Area Computation by the Alternative Coordinate Method01:24

Area Computation by the Alternative Coordinate Method

200
The alternative coordinate method, also known as the Shoelace Formula, is a technique for determining the area of a traverse using Cartesian coordinates. This method relies on the sequential arrangement of x and y coordinates for each point of the shape, ensuring accuracy and ease of application.In this approach, each corner's x and y coordinates are listed as fractions, with the x-coordinate as the numerator and the y-coordinate as the denominator. These coordinates are arranged sequentially...
200
Three-Dimensional Force System:Problem Solving01:30

Three-Dimensional Force System:Problem Solving

946
A three-dimensional force system refers to a scenario in which three forces act simultaneously in three different directions. This type of problem is commonly encountered in physics and engineering, where it is necessary to calculate the resultant force on the system, which can then be used to predict or analyze the behavior of the object or structure under consideration.
To solve a three-dimensional force system, first resolve each force into its respective scalar components. Do this using...
946
Two-Dimensional Force System: Problem Solving01:29

Two-Dimensional Force System: Problem Solving

747
Solving problems related to two-dimensional force systems is an essential aspect of mechanics and engineering. By applying the principles of vector analysis and force equilibrium, one can determine the effect of multiple forces acting on an object in a two-dimensional space.
The first step to solving a two-dimensional force system problem is to draw a free-body diagram of the object under consideration. This diagram helps identify all the external forces acting on the object, including their...
747
Theorems of Pappus and Guldinus: Problem Solving01:12

Theorems of Pappus and Guldinus: Problem Solving

829
Pappus and Guldinus's theorems are powerful mathematical principles that are used for finding the surface area and volume of composite shapes. For example, consider a cylindrical storage tank with a conical top. Finding the surface area or volume can be challenging for such complex shapes. These theorems are particularly useful in calculating the volume and surface area of such systems. Here, the cylindrical storage tank with a conical top can be broken down into two simple shapes: a...
829

You might also read

Related Articles

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

Sort by
Same author

Multiscale machine learning molecular mechanics for mechanism and stereoselectivity of Diels-Alderase catalysis.

Nature communications·2026
Same author

Development and Test of Highly Accurate End Point Free Energy Methods. 4. Expanding Solvents Capability and logBB Prediction.

The journal of physical chemistry. B·2026
Same author

K16F/E22F Mutation Promotes Oligomerization and Alters β-Sheet Topology of Aβ16-22 Peptides: Insights from Molecular Dynamics Simulations.

ACS chemical neuroscience·2026
Same author

A Comparative Study of Deep Learning and Classical Modeling Approaches for Protein-Ligand Binding Pose and Affinity Prediction in Coronavirus Main Proteases.

Journal of chemical information and modeling·2025
Same author

TorchANI-Amber: Bridging Neural Network Potentials and Classical Biomolecular Simulations.

The journal of physical chemistry. B·2025
Same author

Accurate site-specific folding via conditional diffusion based on AlphaFold3.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same journal

Multilevel Fragmentation and Boundary Corrections for Accurate Vibrational Spectra of Large Molecules.

Journal of chemical theory and computation·2026
Same journal

Special Topics: Developments of Theoretical and Computational Chemistry Methods in Asia.

Journal of chemical theory and computation·2026
Same journal

Predicting Excited-State Energies from Ground-State Descriptors in Thermally Fluctuating π-Conjugated Molecules.

Journal of chemical theory and computation·2026
Same journal

Many-Body Theory Predictions of Positron Binding Energies in Five-Membered Heterocycles Involving N, O, S, and NH Substituents.

Journal of chemical theory and computation·2026
Same journal

<i>opt</i>-DDAP: Optimizable Density-Derived Atomic Point Charges via Automatic Differentiation.

Journal of chemical theory and computation·2026
Same journal

A Force-Kernel Reformulation of the Extended-System Adaptive Biasing Force for Free-Energy Calculations.

Journal of chemical theory and computation·2026
See all related articles

Related Experiment Video

Updated: Oct 7, 2025

Spatial Multiobjective Optimization of Agricultural Conservation Practices using a SWAT Model and an Evolutionary Algorithm
11:53

Spatial Multiobjective Optimization of Agricultural Conservation Practices using a SWAT Model and an Evolutionary Algorithm

Published on: December 9, 2012

13.1K

Development and Evaluation of Geometry Optimization Algorithms in Conjunction with ANI Potentials.

Dongxiao Hao1,2, Xibing He1, Adrian E Roitberg3

  • 1Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States.

Journal of Chemical Theory and Computation
|January 12, 2022
PubMed
Summary
This summary is machine-generated.

This study introduces a computational protocol for generating molecular mechanical force field (MMFF) parameters using the active learning potential (ANI-1x). The method efficiently produces accurate torsional potential energy surfaces (PESs) and molecular geometries, crucial for MMFF development.

More Related Videos

The Modular Design and Production of an Intelligent Robot Based on a Closed-Loop Control Strategy
11:53

The Modular Design and Production of an Intelligent Robot Based on a Closed-Loop Control Strategy

Published on: October 14, 2017

11.8K
Design and Optimization Strategies of a High-Performance Vented Box
14:23

Design and Optimization Strategies of a High-Performance Vented Box

Published on: June 9, 2023

1.3K

Related Experiment Videos

Last Updated: Oct 7, 2025

Spatial Multiobjective Optimization of Agricultural Conservation Practices using a SWAT Model and an Evolutionary Algorithm
11:53

Spatial Multiobjective Optimization of Agricultural Conservation Practices using a SWAT Model and an Evolutionary Algorithm

Published on: December 9, 2012

13.1K
The Modular Design and Production of an Intelligent Robot Based on a Closed-Loop Control Strategy
11:53

The Modular Design and Production of an Intelligent Robot Based on a Closed-Loop Control Strategy

Published on: October 14, 2017

11.8K
Design and Optimization Strategies of a High-Performance Vented Box
14:23

Design and Optimization Strategies of a High-Performance Vented Box

Published on: June 9, 2023

1.3K

Area of Science:

  • Computational Chemistry
  • Molecular Mechanics
  • Quantum Chemistry

Background:

  • Molecular mechanical force fields (MMFFs) require accurate torsional angle parameters, often derived from computationally expensive *ab initio* calculations.
  • Active learning potentials (ANI-1x) offer an efficient and accurate alternative for generating potential energy surfaces (PESs).

Purpose of the Study:

  • To develop and assess a computational protocol for MMFF parameterization using ANI-1x, focusing on constrained geometry optimization.
  • To evaluate the performance of ANI-1x with various optimization algorithms for reproducing DFT energies and geometries.

Main Methods:

  • Developed a computational protocol for constrained geometry optimization using force projection for Cartesian coordinates.
  • Assessed ANI-1x with Conjugate Gradient (CG) and quasi-Newton algorithms (BFGS, L-BFGS) for geometry optimization.
  • Performed large-scale assessments on drug molecules and organic molecules for MMFF development.

Main Results:

  • Achieved an average root-mean-square error (RMSE) of 1.3 kcal/mol between ANI-1x and DFT for drug molecule optimizations.
  • Generated torsional PESs with an RMSE of 1.23 kcal/mol for conformers.
  • Demonstrated that CG algorithms with ANI-1x accurately reproduce DFT-optimized geometries and torsional PESs.

Conclusions:

  • The developed computational protocol and algorithms are effective for MMFF parameterization.
  • CG-BS and CG-WS are suitable for generating PESs, while CG-WS or BFGS are ideal for full geometry optimization.
  • This work provides a foundation for improving small-molecule MMFFs with advanced computational methods.