Tags: molecular dynamics

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 (81-100 of 139)

  1. Molecular Dynamics Showcase

    06 Jul 2013 | | Contributor(s):: Michael McLennan, Chen-Yu Li, john stone, Aleksei Aksimentiev, George A. Howlett

    View interesting features of a molecular dynamics trajectory file

  2. 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.

  3. 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...

  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. Molecular Workbench: An Interface to the Molecular World

    25 Jun 2006 | | Contributor(s):: Charles Xie

    The Molecular Workbench software is a free, open-source modeling and authoring program specifically designed for use in science education. Powered by a set of real-time molecular simulation engines that compute and visualize the motion of particles interacting through force fields, in both 2D and...

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. MSE 597G An Introduction to Molecular Dynamics

    13 Nov 2008 | | Contributor(s):: Alejandro Strachan

    The goal of this short course is to provide an introduction to the theory and algorithms behind MD simulations, describe some of the most exciting recent developments in the field and exemplify with a few applications applications. The series also includes a tutorial on the nanoMATERIALS...

  13. MSE 597G Lecture 1: Classical Mechanics

    11 Nov 2008 | | Contributor(s):: Alejandro Strachan

    Basic physics: classical mechanics

  14. MSE 597G Lecture 2: Statistical Mechanics I

    11 Nov 2008 | | Contributor(s):: Alejandro Strachan

    Basic physics: statistical mechanics.

  15. MSE 597G Lecture 3: Statistical Mechanics II

    14 Nov 2008 | | Contributor(s):: Alejandro Strachan

    Basic physics: statistical mechanics, Algorithms: Integrating the equations of motion.

  16. MSE 597G Lecture 4: Interatomic potentials I

    14 Nov 2008 | | Contributor(s):: Alejandro Strachan

    Interatomic potentials: pairwise potentials.

  17. MSE 597G Lecture 5: Interatomic potentials II

    13 Nov 2008 | | Contributor(s):: Alejandro Strachan

    Embedded atom model for metals,Three body terms for semiconductors: Stillinger-Weber,Electrostatics and Covalent interactions.

  18. MSE 597G Lecture 6: Interatomic potentials III

    12 Nov 2008 | | Contributor(s):: Alejandro Strachan

    Reactive force fields,Parameterization of interatomic potentials

  19. MSE 597G Lecture 7: Advanced Techniques for Molecular Dynamics Simulations

    12 Nov 2008 | | Contributor(s):: Alejandro Strachan

    Thermostats and barostats,Linear methods for energy and force calculations,Coarse graining or mesodynamics,Validation and Verification.

  20. MSE 597G: An Introduction to Molecular Dynamics

    13 Nov 2008 | | Contributor(s):: Alejandro Strachan