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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...
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...
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...
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
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...
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.
20 Jul 2017 | | Contributor(s):: Joseph Anderson
Simulate molecular dynamics using LAMMPS as well as an addition electrochemical force field (EChemDID)
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...
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
Change simulation box once in LAMMPS
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...
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
What are the Dreiding paramters for graphene ?
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,...
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.
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
Brenden William Hamilton
Error message: Can’t find file log.lammps
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...
27 Mar 2014 | | Contributor(s):: Benjamin P Haley
Run LAMMPS by uploading a data file and command script.
Luis César Aliaga