The 2.12 release of the molecular dynamics program NAMD (externer Link, öffnet neues Fenster) provides major enhancements in performance, flexibility, and accuracy, complementing the greatly enhanced usability provided by the QwikMD GUI (externer Link, öffnet neues Fenster) released in VMD 1.9.3 (externer Link, öffnet neues Fenster). NVIDIA GPU-accelerated simulations with NAMD 2.12 are up to three times as fast as 2.11, particularly for implicit solvent simulations and single-node simulations of smaller systems. NAMD 2.12 is also optimized for the new Intel Xeon Phi KNL processors found in Argonne Theta (externer Link, öffnet neues Fenster), NERSC Cori (externer Link, öffnet neues Fenster), and TACC Stampede 2 (externer Link, öffnet neues Fenster). NAMD 2.12 builds on the asynchronous multi-copy scripting capabilities introduced in NAMD 2.11 (externer Link, öffnet neues Fenster) with the ability to modify and reload the molecular structure, enabling development of grand canonical and constant pH ensemble methods, as well as an optional Python interface for advanced on-the-fly analysis. Finally, NAMD 2.12 provides a complete, no-recompilation-needed interface for hybrid QM/MM (externer Link, öffnet neues Fenster) with both the semi-empirical code MOPAC and the ab initio/DFT code ORCA. More on new features in the 2.12 release of NAMD can be found here (externer Link, öffnet neues Fenster). NAMD is available free-of-charge as source code, precompiled binaries, pre-installed at supercomputer centers, and now jointly with VMD as one-click interactive molecular modeling (externer Link, öffnet neues Fenster) on the Amazon cloud.
