April 6, 2012

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 2.9b3 has many advantages over NAMD 2.8, among these are:

- Improved (temperature/Hamiltonian) replica-exchange implementation

- Replica-based umbrella sampling via collective variables module

- Optimized shared-memory single-node and multiple-node CUDA builds

- CUDA GPU-accelerated generalized Born implicit solvent (GBIS) model

- CUDA GPU-accelerated energy evaluation and minimization

- Native CRAY XE/XK uGNI network layer implementation

- Faster grid forces and lower-accuracy "lite" implementation

- Hybrid MD with knowledge-based Go forces to drive folding

- Linear combination of pairwise overlaps (LCPO) SASA for GBIS model

- Weeks-Chandler-Anderson decomposition for alchemical FEP simulations

- Collective variables module improvements

- Updates to CUDA 4.0 and Tcl 8.5.9, plus option to build with FFTW 3

- Enhanced performance and scalability

Details at http://www.ks.uiuc.edu/Research/namd/2.9/features.html

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 namd@ks.uiuc.edu.

We are eager to hear from you, and thank you for using our software!