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LAMMPS Data-File Generator
24 Oct 2017 | Tools | Contributor(s): Carlos Miguel Patiño, Lorena Alzate-Vargas, Chunyu Li, Benjamin P Haley, Alejandro Strachan
This tool generates all necessary input files for LAMMPS simulations of molecular systems starting with an atomistic structure.
Atomistic Polymer Workflow Notebook
19 Oct 2017 | Tools | Contributor(s): Benjamin P Haley
Run PolymerModeler and nuSIMM tools to create atomistic polymer systems
22 Aug 2017 | Tools | Contributor(s): Luca Bergamasco, Matteo Fasano, Eliodoro Chiavazzo, Pietro Asinari, Annalisa Cardellini, Matteo Morciano
Compute thermal conductivity of single-walled carbon nano-tubes via NEMD method
Applying Machine Learning to Computational Chemistry: Can We Predict Molecular Properties Faster without Compromising Accuracy?
14 Aug 2017 | Presentation Materials | 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...
Structure-Force Field Generator for Molecular Dynamics Simulations
07 Aug 2017 | Online Presentations | Contributor(s): Carlos Miguel Patiño, Lorena Alzate-Vargas, Alejandro Strachan
Atomistic and molecular simulations have become an important research field due to the progress made in computer performance and the necessity of new and improved materials. Despite this, first...
Multiscale Modelling of Nanoparticle Suspensions
12 Jun 2017 | Online Presentations | Contributor(s): Pietro Asinari
In the present work a multiscale modelling approach is implemented to relate the nanoscale phenomena to the macroscopic bulk properties of nano-suspensions. Specifically, Molecular Dynamics (MD)...
Glass transition temperature notebook
23 May 2017 | Tools | Contributor(s): Benjamin P Haley, Lorena Alzate-Vargas
Calculate the glass transition temperature of an atomistic, amorphous system by running MD simulations in a notebook
Vacancy Formation Energy with MD
08 May 2017 | Tools | Contributor(s): Sam Reeve, Alejandro Strachan
Calculate vacancy formation energy with molecular dynamics and various atomic interaction models
PREPRINT: Molecular Modeling of the Microstructure Evolution during the Carbonization of PAN-Based Carbon Fibers
23 Mar 2017 | Papers | Contributor(s): Alejandro Strachan, Saaketh Desai
Development of high strength carbon fibers (CFs) requires an understanding of the relationship between the processing conditions, microstructure and resulting properties. We developed...
Introduction to Molecular Dynamics Showcase
13 Feb 2017 | Downloads | Contributor(s): Chen-Yu Li, Karl Steven Decker (editor), Aleksei Aksimentiev
In this tutorial, we will demonstrate how to use the MD showcase builder tool to create a showcase. We will start from the simplest example – creating a showcase from a PDB file –...
Fundamentals of Phonon Transport Modeling L1: Introduction
04 Jan 2017 | Presentation Materials | 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 | Presentation Materials | Contributor(s): Xiulin Ruan, Alan McGaughey
LAMMPS structure generator
07 Nov 2016 | Tools | Contributor(s): Benjamin P Haley
Convert a molecular structure file to a LAMMPS data file with force field parameters
28 Oct 2016 | Tools | Contributor(s): Benjamin P Haley, Dan Karls, Alejandro Strachan, Ryan S Elliott, Ellad B Tadmor
Query the OpenKIM repository for names of interatomic Models for simulating selected materials
Coarse Graining of Crystalline Cellulose
24 Oct 2016 | Tools | Contributor(s): Kuo Tian, Mehdi Shishehbor, Pablo Daniel Zavattieri
Bio-inspired Crystalline Nano-Cellulose coarse graining toolkit
Polymer Synthesis and Characterization in the Cloud: a nanoHUB Classroom Experience
22 Jan 2016 | Online Presentations | Contributor(s): Coray Colina
In this talk, I’ll share the experience of teaching a junior undergraduate computational course in materials science and engineering, with over 70 participants. Both molecular and continuum...
MD simulations of shock loading
29 Dec 2015 | Tools | Contributor(s): edwin alberto antillon, Mitchell Anthony Wood, Mathew Joseph Cherukara, Alejandro Strachan
Use MD simulation to study shocks in various materials including metals and energetics
Molecular Exploration Tool
10 Dec 2015 | Tools | Contributor(s): Xueying Wang, nicolas onofrio, Alejandro Strachan, David M Guzman
The tool can display the molecule structures and run Lammps simulations.
Molecular Dynamics Showcase Builder
09 Nov 2015 | Tools | Contributor(s): Michael McLennan, Nicholas K Kisseberth, George A. Howlett, Jim Slopsema, Aleksei Aksimentiev, Chen-Yu Li
Tool to create showcases for the Molecular Dynamics Showcase viewer.
Atomistic Modeling: Past, Present, and Future, MGI, ICME, etc.
03 Nov 2015 | Online Presentations | Contributor(s): Paul Saxe
I will present a perspective on atomistic modeling — tools using quantum methods such as DFT, as well as molecular dynamics and Monte Carlo methods based on forcefields — over the past...