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Visualizing LAMMPS molecular dynamics trajectories using visual molecular dynamics (VMD)

Nuwan Dewapriya's picture

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/1.0072708) 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.

 

Video 1: Fracture of an armchair graphene sheet. 

Video 2: Fracture of a zigzag graphene sheet.   

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