NAMD 2.10 Announcement
December 11, 2014
The Theoretical and Computational Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Institute of General Medical Sciences.
NAMD 2.10 has many advantages over NAMD 2.9, among these are:
- Network topology adaptation for CRAY XE/XK and IBM Blue Gene/Q
- CRAY XC30 and IBM Blue Gene/Q native network layers
- Multiple-copy algorithm support for native network layers
- Lambda-exchange multiple-copy alchemical free energy calculations
- String method with swarms-of-trajectories transition pathways
- Atom coordinate/velocity exchange for multiple-copy algorithms
- Tcl scripting command to reinitialize atoms from output files
- Tcl scripting configuration file parameter introspection
- Tcl scripting trajectory and restart output file switching
- Multilevel summation method for long-range electrostatics
- Normalized external electric field to avoid pressure artifacts
- Improved scalability for collective variables, Tcl forces, etc.
- Collective variables module improvements
- Drude polarizable force field improvements
- SMOG structure-based potential support
- Minimizer stability and performance improvements
- Various improvements for 100-million-atom simulations
- Update to CUDA 6.0 with Kepler GPU optimizations
- GPU-accelerated particle-mesh Ewald calculation
- Intel Xeon Phi coprocessor support
- 64-bit Windows shared-memory single-node port with CUDA support
- 32-bit and 64-bit ARM processor Linux port with CUDA support
- CUDA support for POWER processor Linux port
- Enhanced performance and scalability
NAMD is available from http://www.ks.uiuc.edu/Research/namd/
For your convenience, NAMD has been ported to and will be installed on the machines at the NSF-sponsored national supercomputing centers. If you are planning substantial simulation work of an academic nature you should apply for these resources. Benchmarks for your proposal are available at http://www.ks.uiuc.edu/Research/namd/performance.html
The Theoretical and Computational Biophysics Group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to email@example.com.
We are eager to hear from you, and thank you for using our software!