Molecular Dynamics Simulations
Molecular Dynamics Simulations - Related Videos
06:37
Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
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Cited by 2 •
2021
Melts and fluids are ubiquitous vectors of mass transport in natural systems. We have developed an open-source package to analyze ab initio molecular-dynamics simulations of such systems. We compute structural (bonding, clusterization, chemical speciation), transport (diffusion, viscosity) and thermodynamic properties (vibrational spectrum).
12:39
Computational Fluid Dynamics Simulations of Blood Flow in a Cerebral Aneurysm
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2023
Source: Joseph C. Muskat, Vitaliy L. Rayz, and Craig J. Goergen, Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana The objective of this video is to describe recent advancements of computational fluid dynamic (CFD) simulations based on patient- or animal-specific vasculature. Here, subject-based vessel segmentations were created, and, using a combination of open-source and commercial tools, a high-resolution numerical solution was determined within a flow model.
15:05
Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
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Cited by 7 •
2020
The objective of this protocol is to use molecular dynamics simulations to examine the dynamic structural changes that occur due to activating mutations of the EGFR kinase protein.
13:58
Probing C84-embedded Si Substrate Using Scanning Probe Microscopy and Molecular Dynamics
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Cited by 1 •
2016
This paper reports the nanomaterial fabrication of a fullerene Si substrate inspected and verified by nanomeasurements and molecular dynamic simulation.
05:57
Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
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2024
Here, we describe a protocol for the optimization and parameterization of amino acid residues modified with reactive carbonyl species, adaptable to protein systems. The protocol steps include structure design and optimization, charge assignments, parameter construction, and preparation of protein systems.
FAQs
An interatomic potential describes how the energy of an atomic arrangement changes with the positions of its atoms. The simulation derives forces from this potential, then uses those forces to update atomic motion. Because the potential governs interactions throughout the calculation, its suitability strongly influences predicted strength, diffusion, stability, and thermal transport in the modeled material.
The time step controls how frequently the calculation updates atomic positions and velocities while integrating Newton’s equations. It must be small enough to represent motion accurately under the selected interatomic potential. Repeating these updates produces a trajectory that can be analyzed for evolving structure and material behavior, whereas unsuitable time resolution can undermine the reliability of the modeled dynamics.
Temperature, pressure, and boundary conditions define the physical environment represented by the calculation. Changing them can alter atomic motion, structural stability, transport behavior, and the response of a material or fluid system. Specifying these conditions allows engineers to examine how a system behaves under different operating or constraint scenarios rather than treating one trajectory as universally representative.
A trajectory records the time-dependent microscopic motions generated during the simulation, allowing researchers to examine mechanisms behind an observed property. It can connect local atomic interactions with outcomes such as diffusion, strength, stability, or thermal transport. This mechanistic view helps explain why a material behaves as it does, including processes that experiments may not resolve directly.
A study begins by defining the material or fluid system, selecting an interatomic potential, and specifying temperature, pressure, boundary conditions, and other constraints. The calculation then advances the atoms through many small integration steps to generate a trajectory. Engineers analyze that trajectory to estimate relevant properties and interpret the microscopic mechanisms associated with the result.
Applications include materials, surfaces, polymers, nanostructures, and fluid systems. In these settings, the approach can support design and evaluation by examining strength, diffusion, stability, and thermal transport at the atomistic level. Its usefulness extends from understanding material response to comparing how structures or operating conditions may influence performance and process optimization.