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LAMMPS Structure Analysis Toolkit
01 Aug 2018 | Contributor(s):: Nicholas J Finan, Saaketh Desai, Sam Reeve, Alejandro Strachan
Perform structural analysis on trajectories in LAMMPS dump format
Shobhit Sanjeev Chaturvedi
Sumit Kumar Sinha
Serge Raymond Maalouf
LAMMPS Data-File Generator
01 Aug 2017 | | 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 | | Contributor(s):: Benjamin P Haley
Run PolymerModeler and nuSIMM tools to create atomistic polymer systems
23 May 2017 | | 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?
26 Jul 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...
Structure-Force Field Generator for Molecular Dynamics Simulations
01 Aug 2017 | | 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 principle simulations of large molecules are still not possible because the high computational time...
Multiscale Modelling of Nanoparticle Suspensions
09 Jun 2017 | | 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) simulations and Brownian Dynamics (BD) are synergistically integrated to understand the mechanisms...
Glass transition temperature notebook
22 May 2017 | | 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
03 May 2017 | | 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 | | Contributor(s):: Alejandro Strachan, Saaketh Desai
PREPRINTDevelopment of high strength carbon fibers (CFs) requires an understanding of the relationship between the processing conditions, microstructure and resulting properties. We developed a molecular model that combines kinetic Monte Carlo (KMC) and molecular dynamics (MD) techniques to...
Introduction to Molecular Dynamics Showcase
10 Feb 2017 | | 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 – and move on to more complicated examples. We will also cover how to add a description, change...
Fundamentals of Phonon Transport Modeling L1: Introduction
03 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
03 Jan 2017 | | Contributor(s):: Xiulin Ruan, Alan McGaughey
LAMMPS structure generator
01 Nov 2016 | | Contributor(s):: Benjamin P Haley
Convert a molecular structure file to a LAMMPS data file with force field parameters