The Design and Implementation of the VMD Plugin for NAMD Simulations on the Amazon Cloud

Abstract

High Performance Computing (HPC) clusters have enabled Molecular Dynamics (MD) simulations of biological systems for a sufficiently large complexity and long simulation period. VMD and NAMD are two major MD simulations software packages, which can work together for mining structural information of bio-molecules. However, HPC clusters are in many cases unaffordable and when accessed force users to wait long time for the results of their computations. Recent years, clouds have provided HPC clusters on demand that allow users to benefit from their flexibility, elasticity, provision services on demand and flexible pay-as-you-go payment method. Although cloud computing promises to provide seamless access to HPC clusters through abstractions of services that hide the details of the underlying software and hardware infrastructure, users without in depth computing knowledge are still forced to cope with many low level details. Therefore, we have designed and developed a software plugin of VMD, which can provide an integrated framework for VMD and NAMD to be executed on Amazon EC2 cloud. The proposed Amazon EC2 Plugin for VMD frees users from performing many tedious computing tasks such as launching, connecting and terminating Amazon EC2 compute instances; configuring a HPC cluster; and installing middleware and software applications before the system is readily available for any scientific investigation. Thus, it allows VMD/NAMD users to spend less time getting applications to work on HPC clusters but more time on researching.