VMD

I would like to share the codes required to perform an end-to-end molecular dynamics simulation, which will be useful to the novice researchers in the filed of atomistic simulations. I focus on simulating uniaxial tensile tests of a graphene sample in the LAMMPS molecular dynamics simulator, and I have attached two MATLAB scripts to create the input files for LAMMPS and to extract data from the LAMMPS output file.

A PhD position is open for summer or fall 2017 in Advanced Hierarchical Materials by Design Lab at Louisiana Tech University on multiscale modeling of hierarchical materials with an emphasis on nanocomposites. The candidates must have earned a M.Sc. degree in Mechanical Engineering or related fields and have a solid background in theoretical and computational mechanics, specifically continuum mechanics and finite element modeling, and need to have the knowledge of writing computer code (preferably using C/C++).

Dr. Axel Kohlmeyer , one of the LAMMPS code developers, is organizing FREE School on Molecular Dynamics for Biomolecules and Nanomaterials at Temple University, Philadelphia (August 18th - 22nd, 2014)

 Detail Schedule is Available Here 

I would like to share with you our recent paper published in the Journal of Applied Mechanics: J. Appl. Mech. 81(8), 081010 (Jun 02, 2014)

Abstract

It is very important to visualize molecular dynamics (MD) trajectories since there are many aspects of MD simulations which are difficult to identify without a proper visualization tool. Improper bounday condition in MD is one of such examples. I use Visual Molecular Dynamics (VMD) to visualize my MD simulations. Some of my movies, created using VMD, are shown below.