NAMD 2.9 Goes Viral on Blue Waters
Viruses reproduce by splicing their genetic material into a host cell, causing the cell to manufacture new viruses. This genetic material is protected outside of the host cell by a protein capsid, which disassembles inside a new cell to complete the infection process. Simulation of viral infection has progressed significantly since the first all-atom virus simulation was done with NAMD in 2006 and is one of the driving biomedical projects for the software. A new collaboration with the Pittsburgh Center for HIV Protein Interactions has applied molecular dynamics flexible fitting to construct the first all-atom structure of an HIV virus capsid in its tubular form (shown). This structure is now being simulated as one of six early science projects on the Blue Waters petascale supercomputer being installed at Illinois. These large-scale simulations are enabled by the 2.9 release of NAMD, which includes a new high-performance interface to the Cray Gemini network of Blue Waters. Smaller simulations may also leverage petascale computing through a new replica-exchange framework that supports parallel tempering and integrates with the collective variables module for umbrella sampling conformational free energy calculations. GPU acceleration enhancements include minimization and implicit solvent support as well as exploitation of shared memory, extending performance gains to the desktop.