This thesis has contributed to the literature by providing a pathway to simplify the process of carrying out molecular dynamics simulation. As a part of the investigation, a user-friendly vision-augmented technique was developed to set up and carry out atomistic simulations using hand-gestures. The system is novel in its concept as it enables the user to directly manipulate the atomic structures on the screen, in 3D space using hand gestures, allowing the exploration and visualisation of molecular interactions at different relative conformations. The hand gestures are used to pick and place atoms on the screen allowing thereby the ease of preparing and carrying out molecular dynamics simulations in a more intuitive way. The end result is that users with limited expertise in developing molecular structures can now do so easily and intuitively by the use of body gestures to interact with the simulator to study the system in question. The proposed system was tested by performing parallel molecular dynamics simulations to study (i) crystal anisotropy of a diamond cubic substrate (crystalline silicon) using nanoindentation with a long-range (Screened bond order) Tersoff potential and (ii) crystal anisotropy of a body centre cubic metal (tantalum) using nanoindentation with an Embedded Atomic Method (EAM) type potential. The MD data was post-processed to reveal size effects observed in anisotropy of both these materials, namely, silicon and tantalum. The value of hardness and elastic modulus obtained from the MD data was found in accordance with what has been discovered previously by experiments, thereby validating the simulations. Based on this, it is anticipated that the proposed system will open up new horizons to the current methods on how an MD simulation is designed and executed.