LAMMPS: Strategy for Molecular Dynamics Simulation
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