Energy optimization using LAMMPS

LAMMPS LAMMPS Beginners
1

Hi

I’m a new user on LAMMPS. And I have one project I want to simulate my data by using it.
What is the best channels to begin (YouTube, books, videos, …)?

Also, In my project I want to add “metal ion” to Metal-Organic Framework (MOF), then make energy optimization for structure relaxation, so that each atom will get the correct site positions. How I can do this process? and what are the steps? There are any specific tutorials for this?

Many thanks

2

Hi,

The LAMMPS official website has a list of tutorials there: LAMMPS Tutorials as well as a list of recommended books: Books about Molecular Dynamics generally or LAMMPS specifically. This is where I would start.

Simon

3

Thank you for your reply.

What about adding “metal ion” to Metal-Organic Framework (MOF), then make energy optimization for structure relaxation, so that each atom will get the correct site positions. How I can do this process? and what are the steps? There are any specific tutorials for this?

Many thanks

4

Before you can do your research project, you first have to become familiar with the MD simulation tools and the basics of MD simulations. Skipping this step and jumping immediately to starting your research is a very bad idea. Doing MD simulations is as much a craft as it is a science.

Think about this the following way: how does one become a craftsman, say a carpenter? You don’t start by building a complex cabinet, but rather with simple things like boxes and tables where you learn how to properly use the tools of the trade and get a feeling for the material you are working with. The same applies to learning MD simulation.

Please also keep in mind that if there was a tutorial for your specific research project, then there would be no more need to do research on that subject. Thus the best you can do is to search the published literature for something similar and learn from that. But those kinds of publications usually describe the systems setup for people that already know how to do MD simulations and that puts you back to square one: learning the basics first and then gradually add complexity and improve your skills until they are good enough and you understand what is given in the publications.