Tags: molecular dynamics (MD)

Description

Molecular dynamics is a form of computer simulation in which atoms and molecules are allowed to interact for a period of time by approximations of known physics, giving a view of the motion of the particles. This kind of simulation is frequently used in the study of proteins and biomolecules, as well as in materials science. More information on Molecular dynamics can be found here.

Resources (61-80 of 185)

  1. LegoGen

    05 Feb 2016 | | Contributor(s):: Scott Michael Louis Slone, Chris Maffeo, AbderRahman N Sobh, Aleksei Aksimentiev

    Tool workflow for building DNA Brick structures automatically.

  2. Polymer Synthesis and Characterization in the Cloud: a nanoHUB Classroom Experience

    31 Aug 2015 | | 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 methods were studied and applied to relevant materials problems. Students were able to build and...

  3. MD simulations of shock loading

    11 Jun 2015 | | 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

  4. Molecular Exploration Tool

    01 Aug 2014 | | Contributor(s):: Xueying Wang, nicolas onofrio, Alejandro Strachan, David M Guzman

    The tool can display the molecule structures and run Lammps simulations.

  5. Tensile Testing Laboratory: Nanoscale and Macroscale Metal Samples

    24 Nov 2015 | | Contributor(s):: Aisling Coughlan, Kendra A. Erk, David Ray Johnson, Tanya Faltens, Alejandro Strachan, Heidi A Diefes-Dux

    This document is an updated (Fall 2015) sophomore materials science and engineering tensile testing laboratory handout that introduces students to the atomic-level processes that are responsible for plastic deformation. By performing standard tensile tests on a ductile metal in conjunction with...

  6. Molecular Dynamics Showcase Builder

    09 Nov 2015 | | 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.

  7. Atomistic Modeling: Past, Present, and Future, MGI, ICME, etc.

    03 Nov 2015 | | 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 30 years or so. While we are all caught up in the present, it is important to remember and realize...

  8. Introduction to Molecular Dynamics

    27 Aug 2015 | | Contributor(s):: Alejandro Strachan

  9. Nanomaterial Mechanics Explorer

    30 Jun 2015 | | Contributor(s):: Sam Reeve, Christopher Chow, Michael N Sakano, shuhui tang, Alexis Belessiotis, Mitchell Anthony Wood, Kiettipong Banlusan, Saaketh Desai, Alejandro Strachan

    Simulate dislocation dynamics, crack propagation, nanowire tensile tests, and phase transitions

  10. Introduction to Molecular Dynamics

    06 Apr 2015 | | Contributor(s):: Alejandro Strachan

    This short presentation will describe the idea behind MD simulations and demonstrate its use in real applications.

  11. Reproducing results of "Thermal transport in SiGe superlattice thin films and nanowires"

    27 Mar 2015 | | Contributor(s):: Alejandro Strachan, Jonathan Mark Dunn

    In this document we show how to reproduce results in the paper "Thermal transport in SiGe superlattice thin films and nanowires", Keng-hua Lin, and Alejandro Strachan Physical Review B 87, 115302 (2011) using the nanoMATERIALS nanoscale heat transport tool in nanoHUB....

  12. Tensile Testing of Nanoscale and Macroscale Metal Samples

    25 Mar 2015 | | Contributor(s):: Aisling Coughlan, Kendra A. Erk, David Ray Johnson, Tanya Faltens, Alejandro Strachan, Heidi A Diefes-Dux

    This document is a sophomore materials science and engineering tensile testing laboratory handout (Fall 2014) that introduces students to the atomic-level processes that are responsible for plastic deformation. By performing standard tensile tests on a ductile metal in conjunction with...

  13. MSE 498 Lesson 10: MD

    16 Mar 2015 | | Contributor(s):: Andrew Ferguson

    This new course will give students hands-on experience with popular computational materials science and engineering software through a series of projects in: electronic structure calculation (e.g., VASP), molecular simulation (e.g., GROMACS), phase diagram modeling (e.g., Thermo-Calc), finite...

  14. MSE 498 Lesson 11: MD

    16 Mar 2015 | | Contributor(s):: Andrew Ferguson

    This new course will give students hands-on experience with popular computational materials science and engineering software through a series of projects in: electronic structure calculation (e.g., VASP), molecular simulation (e.g., GROMACS), phase diagram modeling (e.g., Thermo-Calc), finite...

  15. MSE 498 Lesson 12: MD

    16 Mar 2015 | | Contributor(s):: Andrew Ferguson

    This new course will give students hands-on experience with popular computational materials science and engineering software through a series of projects in: electronic structure calculation (e.g., VASP), molecular simulation (e.g., GROMACS), phase diagram modeling (e.g., Thermo-Calc), finite...

  16. MSE 498 Lesson 13: MD

    16 Mar 2015 | | Contributor(s):: Andrew Ferguson

    This new course will give students hands-on experience with popular computational materials science and engineering software through a series of projects in: electronic structure calculation (e.g., VASP), molecular simulation (e.g., GROMACS), phase diagram modeling (e.g., Thermo-Calc), finite...

  17. MSE 498 Lesson 14: MD

    16 Mar 2015 | | Contributor(s):: Andrew Ferguson

    This new course will give students hands-on experience with popular computational materials science and engineering software through a series of projects in: electronic structure calculation (e.g., VASP), molecular simulation (e.g., GROMACS), phase diagram modeling (e.g., Thermo-Calc), finite...

  18. MSE 498 Lesson 15: MD

    16 Mar 2015 | | Contributor(s):: Andrew Ferguson

    This new course will give students hands-on experience with popular computational materials science and engineering software through a series of projects in: electronic structure calculation (e.g., VASP), molecular simulation (e.g., GROMACS), phase diagram modeling (e.g., Thermo-Calc), finite...

  19. Crack Propagation Simulation

    06 Aug 2014 | | Contributor(s):: hojin kim, Nilofer Rajpurkar, Benjamin P Haley, Alejandro Strachan

    Simulate crack propagations through materials under applied loads.

  20. Homework assignment: learning about elastic constants via molecular dynamics simulations

    17 Feb 2015 | | Contributor(s):: Alejandro Strachan, David Ray Johnson

    In this homework assignment students will use molecular dynamics to compute the elastic constants of metals using an embedded atom model to describe atomic interactions. They will deform  a single crystal along different directions and obtain c11, c12 and c44 elastic constants from the...