This is a 5 minutes introduction to molecular dynamics simulation. Tools to generate initial state for your system: - LAMMPS lattice command: This command creates a 2D or 3D lattice. It supports a number of lattice types.
Thanks for this useful and precise video.. I have one question: What potential should be used when we study hydrogen adsorption on another nano-cluster? In this case it seems like bonded potential should be for the nano-cluster and non-bonded potential for hydrogen molecules. Please clarify.
Hi, can you recommend MDS softwares with MM2 for simulation of bonding of chemical compounds of interest with the stationary phase for chromatographic analysis
Thanks for the explanation! As I am a beginner in MD Simulations, I wanted someone to recommend me an MD Software that I can use. Freeware would be more preferred
Thanks for your message. For MD simulations LAMMPS and Gromacs are both good software (depending on the application one can be better than the other). They are both open source and free as well. I have another video where I explain how to start a simulation with LAMMPS.
energy minimizations will run without problem, but simulations will be problematic. Maybe if you include some GPU nodes, that could help, but on CPU only, it is cumbersome
