AbstractVMD and NAMD are two major molecular dynamics simulation software packages, which can work together for mining structural information of bio-molecules. Carrying out such molecular dynamics simulations can help researchers to understand the roles and functions of various bio-molecules in life science research. Recently, clouds have provided HPC clusters on demand that allow users to benefit from their flexibility, elasticity, and lower costs. Although cloud computing promises to provide seamless access to HPC clusters through the abstraction of services, which 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 system and programming details. Therefore, we have designed and developed a software plugin of VMD, which can provide an integrated framework for NAMD to be executed on Amazon EC2. 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. This allows VMD/NAMD users to spend less time getting applications to work on HPC clusters but more time for bio-research.