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 Section 2.6 and Appendix B of my MASC thesis (https://open.library.ubc.ca/cIRcle/collections/ubctheses/24/items/1.007…) give an example of visualizing a graphene nanoribbon using VMD. Furthermore, I share relevent data and input files required for LAMMPS MD simulator in Appendix A of PhD thesis (http://summit.sfu.ca/item/16590#310). I hope thes will be useful for those who would like to learn MD simulations.