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.

Tools (1-20 of 54)

  1. Visualization Dashboard for MPCAs

    Tools | 09 Mar 2022 | Contributor(s):: Juan Carlos Verduzco Gastelum, Zachary D McClure, Alejandro Strachan

    Sim2L Visualization Dashboard for Multi-Principal Component Allloys

  2. Active Learning Workflow for MPCAs

    Tools | 05 Oct 2021 | Contributor(s):: Juan Carlos Verduzco Gastelum, David Enrique Farache, Zachary D McClure, Saaketh Desai, Alejandro Strachan

    Active learning workflow for MPCAs using MD simulation tool MeltHEAS for optimized melting temperatures

  3. MIT Atomic-Scale Modeling Toolkit

    Tools | 15 Jan 2008 | Contributor(s):: David A Strubbe, Enrique Guerrero, daniel richards, Elif Ertekin, Jeffrey C Grossman, Justin Riley

    Tools for Atomic-Scale Modeling

  4. Thermal Conductivity Simulator

    Tools | 03 Oct 2020 | Contributor(s):: Md Shajedul Hoque Thakur, Md Mahbubul Islam

    Simulate thermal conductivity of Silicon using reverse non-equilibrium molecular dynamics simulations.

  5. Refractory Complex Concentrated Alloy Melting Point Calculation

    Tools | 25 May 2020 | Contributor(s):: Zachary D McClure, Saaketh Desai, Alejandro Strachan

    Calculate melting point of BCC-type high entropy alloys through phase coexistence method

  6. Unsupervised learning using dimensionality reduction via matrix decomposition

    Tools | 01 Apr 2020 | Contributor(s):: Michael N Sakano, Alejandro Strachan

    Learn PCA and NMF via chemistry example

  7. High Entropy Alloy Melting Point Calculation

    Tools | 19 Feb 2020 | Contributor(s):: Zachary D McClure, Saaketh Desai, Alejandro Strachan

    Calculate melting point of high entropy alloys through phase coexistence method

  8. Nanoparticle Shape Lab

    Tools | 23 Dec 2019 | Contributor(s):: JCS Kadupitiya, Nicholas E. Brunk, Vikram Jadhao

    Simulates the low-energy shapes of nanocontainers over a wide range of solution conditions

  9. LAMMPS Input Structure Generator for Functionally Graded Materials (FGM)

    Tools | 17 Nov 2019 | Contributor(s):: Md Shajedul Hoque Thakur, Mahmudul Islam, Abdullah Amin, Satyajit Mojumder, Md Mahbubul Islam

    Generates initial geometries of Functionally Graded Materials (FGM) for LAMMPS simulations

  10. NPT Simulator

    Tools | 20 Aug 2019 | Contributor(s):: Julian C Umeh, Thomas A Manz

    Calculate density and total energy of gas molecules using NPT ensemble

  11. Radial Distribution Function Calculator

    Tools | 18 Jul 2019 | Contributor(s):: Julian C Umeh, Thomas A Manz

    This tools calculates the radial distribution function of gas molecules

  12. Gas Diffusion Coefficient in Metal Organic Frameworks

    Tools | 22 Feb 2019 | Contributor(s):: Julian Chinonso Umeh, Thomas A Manz

    Calculates gas self diffusion coefficient in metal organic frameworks

  13. LAMMPS driver tool for potential calibration

    Tools | 15 Feb 2019 | Contributor(s):: Saaketh Desai, Alejandro Strachan

    Calculates basic properties of interest with a given interatomic potential and is used to drive the calibration of the potential.

  14. Nanoparticle Assembly Lab

    Tools | 22 Jan 2019 | Contributor(s):: Nicholas Brunk, JCS Kadupitiya, Masaki Uchida, Douglas, Trevor, Vikram Jadhao

    Simulate assembly of nanoparticles into aggregates in physiological conditions.

  15. FunUQ for MD

    Tools | 24 Jun 2018 | Contributor(s):: Sam Reeve, Alejandro Strachan

    Functional uncertainty quantification for molecular dynamics

  16. Graphene Nanopore Drilling

    Tools | 26 Feb 2018 | Contributor(s):: Jae Hyun Park, Darren K Adams, Narayan Aluru

    Drilling a nanopore in graphene by Si-nanoparticle bombardment

  17. LAMMPS Structure Analysis Toolkit

    Tools | 07 Dec 2017 | Contributor(s):: Nicholas J Finan, Saaketh Desai, Sam Reeve, Alejandro Strachan

    Perform structural analysis on trajectories in LAMMPS dump format

  18. Nanosphere Electrostatics Lab

    Tools | 03 May 2018 | Contributor(s):: JCS Kadupitiya, Nicholas Brunk, Sohile Ali, Fox, Geoffrey C., Vikram Jadhao

    The Nanosphere Electrostatics Lab empowers users to simulate the self-assembly of ions near a spherically shaped nanoparticle, and extract the effective electrostatic properties.

  19. Focused Ion Beam Molecular Dynamics

    Tools | 01 Dec 2017 | Contributor(s):: Joshua Michael Stout, Sixian Jia

    3-D Molecular Dynamics Simulation of a Gallium FIB on Silicon

  20. Ions in Nanoconfinement

    Tools | 06 Dec 2017 | Contributor(s):: Kadupitige Kadupitiya, Nasim Anousheh, Suresh Marru, Fox, Geoffrey C., Vikram Jadhao

    The Ions in Nanoconfinement app empowers users to simulate ions confined between material surfaces that are nanometers apart, and extract the associated ionic structure.