Nuwan Dewapriya's blog

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.

In appendix A of my PhD thesis, I share a MATLAB code to get coordinates of carbon atoms in a graphene sheet. The code also generates the data file required for LAMMPS. In addition, I included a sample input and the corresponding output files from LAMMPS. I hope this will be useful for those who would like to learn MD simulations.

I would like to share with you my first paper in a SCI journal: doi:10.1088/0965-0393/21/6/065017