All Categories (1-20 of 27)

  1. Structural Analysis for Molecular Dynamics Trajectories

    03 Mar 2019 | | Contributor(s):: Nicholas J Finan, Saaketh Desai, Sam Reeve, Alejandro Strachan

    This tool reads in LAMMPS trajectories and performs the following analysis: Radial Distribution Function (RDF), X-Ray Diffraction (XRD), Vibrational Density of States, and  (More to Come!). By default the tool requires trajectory files to be input by the user however there are some...

  2. Rajmohan Muthaiah


  3. Tabulting potencial LAMMPS

    Closed | Responses: 1


    I have a potential for a molecule which depends on (r, theta, phi), also at different part cell has different variable, is it possible to tabulate such potential in...


  4. 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...

  5. 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

  6. a question about ECHENDID package

    Closed | Responses: 0

    Dear sir / madam

    I want to use ECHEMDID package, I tried ECM example in computers with different CPU numbers, but there is not any change in speed and it takes very long...


  7. 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.

  8. Electrochemical Simulation

    20 Jul 2017 | | Contributor(s):: Joseph Anderson

    Simulate molecular dynamics using LAMMPS as well as an addition electrochemical force field (EChemDID)

  9. 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 and...

  10. 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

  11. Change simulation box once in LAMMPS

    Closed | Responses: 0

    Dear all,

    I have the following problem:

    I generate successfully in Polymer Modeler an initial configuration of PE (degree of polymerization 100, 26 chains) in a box of...


  12. 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

  13. Michael Worku


  14. What are the Dreiding paramters for graphene ?

    Closed | Responses: 1


    I am using lammps to simulate PMMA-graphene composite system. I used polymer modeller to create the PMMA chains. I want to add the graphene sheet but I am not sure what bond_coeff,...


  15. when I runn with my own exe.lammps 3 minimize has done but at fix 1 all nvt temp 300.0 300.0 100.0 this error apear: ERROR: All pair coeffs are not set (../pair.cpp:175) I will be very thankfull.

    Closed | Responses: 1


  16. nuSIMM: nanoHUB user Simulation Interface for Molecular Modeling

    26 May 2015 | | Contributor(s):: Michael Fortunato, Lauren Abbott, Kyle E Hart, coray colina

    Simulated polymerization, equilibration, and characterization of molecular models

  17. Brenden William Hamilton

    PhD student in Materials Engineering at Purdue with a focus in shock response of materials and energetic materials. Current works include energy localization and transport, as well as quantum...


  18. Error message: Can’t find file log.lammps

    Closed | Responses: 1

    I am trying to run a simple test example that I have run before, but all I get is an error message: "Can't find file log.lammps" ... Can't understand the equivalent command...


  19. LAMMPS

    27 Mar 2014 | | Contributor(s):: Benjamin P Haley

    Run LAMMPS by uploading a data file and command script.

  20. Luis César Aliaga