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AutoSolvate (CLI)
14 Aug 2024 | Contributor(s):: Rohit Sai Kiran Gadde, Ariel Gale, Juan Carlos Verduzco Gastelum
Automated workflow to solvate molecules and run QM/MM trajectories
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Lecture 7: Molecular Dynamics Simulation: Calculating Non-bounded Interactions in Real Space
Online Presentations | 25 Jul 2024 | Contributor(s):: Ming Chen
This lecture discusses details about how to calculate non-bounded interactions in real space.
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Lecture 6: Molecular Dynamics Simulation: Common Force Field Forms
Online Presentations | 25 Jul 2024 | Contributor(s):: Ming Chen
This lecture introduce a type of approximated potential energy function: force fields. A set of common function forms used for simulating molecular systems are discussed.
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SMMDS Lectue 5: Potential Energy Function
Online Presentations | 19 Jul 2024 | Contributor(s):: Ming Chen
This lecture introduce the potential energy function used in Lagrangian mechanics and Hamiltonian machanics. Specifically, the lecture introduce how to use quantum mechanics to generate a potential energy function for molecules and materials.
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SMMDS Lecture 4: Hamiltonian Mechanics
Online Presentations | 19 Jul 2024 | Contributor(s):: Ming Chen
This lecture introduce a third formulism of classical mechanics: Hamiltonian Mechanics. Hamiltonian Mechanics provides a fundamental theory for molecular dynamics simulation.
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SMMDS Lecture 3: Lagrangian Mechanics II
Online Presentations | 18 Jul 2024 | Contributor(s):: Ming Chen
This lecture continues the discussion on Lagrangian Mechanics, including discussion on generalized coordinates and some examples.
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SMMDS Lecture 2: Lagrangian Mechanics I
Online Presentations | 17 Jul 2024 | Contributor(s):: Ming Chen
This lecture introduce a different formulism of classical mechanics: Lagrangian mechanics. Lagrangian mechanics provides a systematic way to generate time evolution equations for a many-body system.
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SMMDS Lecture 8: Molecular Dynamics Simulation - Coulomb Interaction and Ewald Summation
Online Presentations | 10 Jul 2024 | Contributor(s):: Ming Chen
This lecture introduce the detailed methods of calculating Coulomb interactions and the Ewald summation method.
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Theories in Statistical Mechanics and Molecular Dynamics Simulations
Courses | 20 Jun 2024 | Contributor(s):: Ming Chen
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SMMDS Lecture 9: Molecular Dynamics Simulation - Ewald Summation
Online Presentations | 20 Jun 2024 | Contributor(s):: Ming Chen
This lecture introduce the detailed theoretical background and implementation of Ewald Summation/Particle Mesh Ewald Summation.
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SMMDS Lecture 1: Introduction
Online Presentations | 03 Jun 2024 | Contributor(s):: Ming Chen
Welcome to the theories in Statistical Mechanics and Molecular Dynamics Simulation! Have you been puzzled on what to learn after elementary statistical mechanics? Have you had questions on why there are so many options in an input file for a MD simulation package? Are you...
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Simplifying Computational Simulations: Using Large Language Models for Automated Research in Materials Science
Online Presentations | 22 May 2024 | Contributor(s):: Ethan Holbrook
In this hands-on workshop, we will explore the transformative role of Large Language Models (LLMs) in computational materials science, emphasizing their integration into the LAMMPS molecular dynamics (MD) simulation framework. ...
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Building a nanoHUB Graphical Interface for Exploring Protein Dynamics and Spectroscopy: the PigmentHunter App
Online Presentations | 18 Apr 2024 | Contributor(s):: Safa Ahad
Running and analyzing protein molecular dynamics (MD) simulations can be time consuming and tedious. In this webinar, we introduce PigmentHunter , an online nanoHUB tool that enables “point-and-click” MD-based simulation of excitonic spectra of chlorophyll proteins based on PDB...
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Thermal Transport in Layered Materials, Devices, and Systems
Online Presentations | 11 Apr 2024 | Contributor(s):: Eric Pop
The thermal properties of layered materials (like graphene and MoS2) are an active area of investigation, particularly due to their anisotropic and tunable thermal conductivity. We have studied their behavior as part of transistors, where self-heating is a major challenge for performance and...
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Deciphering Energy Transfer in Photosynthesis with Multiscale Molecular Modeling
Online Presentations | 07 Dec 2023 | Contributor(s):: Lyudmila V. Slipchenko
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Exploring the Nano World: Building Nanoscale Structures with Polymer Modeler
Online Presentations | 14 Jul 2023 | Contributor(s):: Tongtong Shen
In this talk, I will showcase how atomic-level simulations can lead to a more fundamental understanding of PAN crystal structures and guide you through an interactive Polymer Modeler powered by nanoHUB.
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Teaching and Learning with the MIT Atomic Scale Modeling Toolkit's Classical and Quantum Atomic Modeling Applications
Online Presentations | 23 Dec 2022 | Contributor(s):: Enrique Guerrero
We will perform molecular dynamics computations using LAMMPS, simple Monte Carlo simulations including the Ising model, and run quantum chemistry and density functional theory computations.
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LAMMPS Data File Generator Tool Demo
Online Presentations | 15 Apr 2022 | Contributor(s):: Carlos Miguel Patiño
A quick demonstration of the nanoHUB tool LAMMPS Data-File Generator. This was developed as part of the 2017 NCN URE program.
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Visualization Dashboard for MPCAs
Tools | 09 Mar 2022 | Contributor(s):: Juan Carlos Verduzco Gastelum, Zachary D McClure, Alejandro Strachan
Sim2L Visualization Dashboard for Multi-Principal Component Allloys
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Designing Machine Learning Surrogates for Molecular Dynamics Simulations
Online Presentations | 25 Nov 2021 | Contributor(s):: JCS Kadupitiya
Molecular dynamics (MD) simulations accelerated by high-performance computing (HPC) methods are powerful tools for investigating and extracting the microscopic mechanisms characterizing the properties of soft materials such as self-assembled nanoparticles, virus capsids, confined electrolytes,...