Guides Guides

The typical usage of the workflows by end users can be demonstrated by the example of the integral workflow for MD simulation of tension of metal nanocrystals under different physical conditions with the following steps:

‒        signing into  the IMP Science Gateway;

‒        select and start execution of the workflow;

‒        monitor the current status of execution;

‒        check the MD simulation results obtained by LAMMPS package (tables in the red rectangles in the center of the figure below);

‒        check the MD simulations results converted by Pizza script package for post-processing (table in the red rectangle in the bottom of the figure below);

‒        check the intermediate post-processed visualizations of atomic positions obtained by AtomEye package (images in the top part of the figure below);

‒        check the intermediate post-processed results of X-ray analysis (of the MD simulations results) obtained by Debyer package (tables in the blue rectangles in the bottom part of the figure below);

‒        get the final post-processed results (of the MD simulations results) after X-ray analysis, radial distribution function (RDF) analysis, and stress-strain (SS) analysis obtained by R package (plots in the green rectangles at the left and right sides of the figure below);

‒        get the final post-processed video of visualizations of atomic positions obtained by FFMPEG package (video in the violet rectangle in the top part of the figure below).

 

The integral workflow with the actual MD simulation results, intermediate post-processed data, and final results (plots, visualization images and video).