Design and Implementation of a General Molecular Dynamics Package

Abstract: There are many different codes available for making molecular dynamic simulation. Most of these are focused on high performance mainly. We have moved that focus towards modularity, flexibility and user friendliness. Our goal has been to design a software that is easy to use, can handle many different kind of simulations and is easily extendable to meet new requirements. In the report we present you with the theory that is needed to understand the principles of a molecular dynamics simulation. The four different potentials we have used in the software are presented. Further we give a detailed description of the design and the different design choices we have made while constructing the software. We show some examples of how the software can be used and discuss some aspects of the performance of the implementation. Finally we give our thoughts on the future of the software.