Molecular Dynamics Recipes for Genome Research

Abstract Molecular dynamics (MD)simulation allows one to predict the timeevolution of a systemof interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of modelsystems. MDearnedagreatsuccessin genomeresearch, as it provedto be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on high performance computing (HPC) devices, which are generally expensive and hard to administer. However, variables like the software tool used for modeling and simulation or the size of the molecule under investigation might make one hardware type or configuration more advantageous than another or even makethe commodity hardwaredefinitelysuitablefor MDstudies. This work aims to shedlights on this aspect.