MIssion

The goal of the MDStack project is to develop a distributed molecular dynamics toolbox that allows end scientists to cary our different steps of the MD pipeline on distributed computing resources, mainly XSEDE. Currently the following project are potential users of the MDStack toolbox:

• Binding Affinity Calculation (UCL, P. Coveney, Ole)
• Replica Exchange (Rutgers University, Emilio, Melissa)
• Ensemble/ExTASY (Rice University, Cecilia Clementi, Vivek)

The functional goals of MDStack are defined as follows:

• Allow the execution of different MD tasks (defined below) locally and remotely, including input and output data transfer.
• Provide a simple, homogenous interface (command line tool, API, configuration files) for the different MD tasks.

MD Tasks

• Free Energy Calculation
  • MMPBSA (Amber)

Deadlines and Milestones

The first release of MDStack needs to be ready the first week of May when Cecilia Clementi is visiting our group.