July 6, 2010

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 Center for Research Resources.

NAMD 2.7b3 has many advantages over NAMD 2.6, among these are:

- Collective variable-based calculations

- Improved free energy methods for alchemical transformations

- Grid-based forces and molecular dynamics flexible fitting

- Additional bonded terms for restraining molecular structure

- Support for TIP4P water model

- Support for CHARMM Drude polarizable force field

- Support for C2 long-range electrostatics splitting function

- Support for VDW force switching and long-range tail corrections

- NVIDIA CUDA GPU acceleration of nonbonded force evaluation

- Direct (non-MPI) support for InfiniBand via OFED ibverbs library

- Use of mpirun to launch non-MPI (network or ibverbs) binaries

- Enhanced performance and scalability

Details at http://www.ks.uiuc.edu/Research/namd/2.7/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!