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Structural Analysis for Molecular Dynamics Trajectories
03 Mar 2019 | | Contributor(s):: Nicholas J Finan, Saaketh Desai, Sam Reeve, Alejandro Strachan
This tool reads in LAMMPS trajectories and performs the following analysis: Radial Distribution Function (RDF), X-Ray Diffraction (XRD), Vibrational Density of States, and (More to Come!). By default the tool requires trajectory files to be input by the user however there are some...
Molecular Dynamics Simulation of Displacement Cascade in Molybdenum
06 Dec 2018 | | Contributor(s):: Gyuchul Park, Alejandro Strachan
Displacement cascade in molybdenum was conducted by using Molecular Dynamics (MD) Simulation method. LAMMPS tool was used to run the simulation at nanoHUB. Three primary questions were answered from the simulation:1. The number of displaced atoms/interstitials with respect to time when the...
Combustion in Nanobubbles (generated from water electrolysis)
27 Aug 2018 | | Contributor(s):: Shourya Jain, Li Qiao
A long-pursued goal, which is also a grand challenge, in nanoscience and nanotechnology is to create nanoscale devices, machines and motors that can do useful work. However, loyal to the scaling law, combustion would be impossible at nanoscale be- cause the heat loss would profoundly dominate...
Applying Machine Learning to Computational Chemistry: Can We Predict Molecular Properties Faster without Compromising Accuracy?
14 Aug 2017 | | Contributor(s):: Hanjing Xu, Pradeep Kumar Gurunathan
Non-covalent interactions are crucial in analyzing protein folding and structure, function of DNA and RNA, structures of molecular crystals and aggregates, and many other processes in the fields of biology and chemistry. However, it is time and resource consuming to calculate such interactions...
Fundamentals of Phonon Transport Modeling L1: Introduction
04 Jan 2017 | | Contributor(s):: Alan McGaughey, Xiulin Ruan
Part of the 2016 IMECE Tutorial: Fundamentals of Phonon Transport Modeling: Formulation, Implementation, and Applications.
Fundamentals of Phonon Transport Modeling L2: MD Simulation, Green Kubo, Direct Method
04 Jan 2017 | | Contributor(s):: Xiulin Ruan, Alan McGaughey
Lecture 10: Non Equilibrium MD
05 Jan 2010 | | Contributor(s):: Ashlie Martini
Topics:Calculating transport coefficientShear flowPerturbation methods
Lecture 9: Dynamic Properties
Topics:Time correlation functionsEinstein relationsGreen-Kubo relations
Lecture 8: Static Properties
Topics:Thermodynamic propertiesEntropic propertiesStatic structure
Lecture 7: Initialization and Equilibrium
Topics:Initial positionsInitial velocitiesEvaluating equilibrium
Lecture 6: Neighbor Lists
Topics:Saving simulation timeVerlet listsCell lists
Lecture 5: Boundary Conditions
Topics:Fixed boundariesPeriodic boundary conditionsMinimum image distance
Lecture 4: Temperature Control
Topics:Velocity scalingHeat bath/reservoirStochastic methods
Lecture 3: Integration Algorithms
Topics:General guidelinesVerlet algorithmPredictor-corrector methods
Lecture 2: Potential Energy Functions
Topics:Pair potentialsCoulomb interactionsEmbedded atom modelIntra-molecular interactions (bond, angle, torsion)
Lecture 1: Basic Concepts
Topics:What is MDNewton’s lawBasic concepts and terminology