Abstract
In this chapter, some sample scripts have been provided for giving the readers a basic understanding of scripting using molecular dynamics. After reading this chapter the readers will be able to write their own codes in BIOVIA Materials Studio and Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). Scripts have been provided for calculating the stress-strain response, thermal conductivity, and glass transition temperature using BIOVIA Materials Studio. Scripts have also been provided for molecular dynamics simulation of vacancy formation energy and deformation of a nanowire using LAMMPS. The GROningen MAchine for Chemical Simulations (GROMACS) codes have not been provided here because these are widely available on the link provided in this chapter. The readers are advised to search for these tutorials so that they can get a taste of coding through GROMACS.
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