LAMMPS: Strategy for Molecular Dynamics Simulation

Molecular Dynamics Simulation

Molecular Dynamics Simulation, aka MD simulation, is a computer modelling techniques to simulate, model, and calculate the physical and dynamical properties of atomic and molecular system such as biomolecule, materials, polymer.

A figure on left hand side shows the molecular graphic of Satellite tobacco mosaic virus, rendered in VMD program using Tachyon technique.

Strategy step-by-step

Plan your project

The first step is planning of what you want to do. Read article and literature reviews involving your system and method.

Prepare molecular system and input file

Next, prepare your system and fill molecules into a box. Write input file with suitable parameter and use sensible scientific value.

Do preliminary test and make benchmark

Fine-tune parameters

Run all simulations

Results analysis

Finally,

Tools I generally uses for running molecular dynamics

Prerequisites:

Packmol
Moltemplate
LAMMPS (or others e.g. GROMACS, AMBER, etc.)

Packmol: more to come

Moltemplate: more to come

LAMMPS: one of the most powerful and flexible molecular and multi-scale dynamics simulation software for simulating huge molecular system.

Useful external websites

The followings are some useful links for hands-on tutorials.

Packmol

http://m3g.iqm.unicamp.br/packmol/home.shtml

https://linuxcluster.wordpress.com/category/application/packmol/

https://sites.google.com/site/mdsimulationsatfsu/software/what-is-packmol

https://molsim2.wordpress.com/2017/08/21/packmol-tutorial/

http://www.iitg.ac.in/tamalb/karp/packmol.html

Moltemplate

https://www.moltemplate.org/visual_examples.html

LAMMPS

https://lammps.sandia.gov/tutorials.html

https://icme.hpc.msstate.edu/mediawiki/index.php/LAMMPS_tutorials

https://www.osti.gov/servlets/purl/1377717

https://www.utdallas.edu/~bxw109120/lj17lammps/Lammps_tut.pdf

AMBER

http://ambermd.org/tutorials/advanced/tutorial15/Tutorial2.xhtml

Rangsiman Ketkaew