Required LAMMPS and MATLAB files for several molecular dynamics simulations.

LAMMPS scripts to simulate uniaxial tensile test of a graphene Sample

Contains the MD model used in the article Dewapriya and Miller, J. Appl. Mech. 88(10): 101005 (2021).

This a toolkit repository to read, and analysis ab initio molecular dynamics simulations

Prediction of transition time (kinetics) associated with aromatic ring flipping using infrequent metadynamics

NAMD simulation setup for a an example setup of polypeptide

An implementation of the MM3 molecular dynamics code written in MATLAB

Projects of the numerical part of the course Computational Techniques for Molecular Modeling. Simulations on molecular modelling and molecular dynamics.

Simulation/computation models created for optical physics research

a small framework for simulating molecular dynamics in MATLAB, developed for my master thesis

Molecular modelling of NH4F nanoclusters

Algorithm designed to aggregate non-bounded MD (water) molecules in order to map their parameters into the coarse-grained model.