NAMD now runs on Windows NT. Windows 2000 probably works and Windows 98 might but I'm not promising anything. You can now run NAMD on all those NT machines sit idle at night.
Formerly a serial bottleneck, the particle mesh Ewald FFT and reciprocal space sum have been distributed. Early results have demonstrated speedups on 128 processors of a Cray T3E. The number of processors used may be limited with the "PMEProcessors" parameter.
Under a new license with MIT, FFTW (www.fftw.org) is now included in all release binaries. Users no longer need recompile NAMD themselves to obtain this performance boost. (FFTW is also available under GPL.)
The default minimizer is now based on conjugate gradients and line searches. It is orders of magnitude faster than the old method, which is still available via the "velocityQuenching" option. If you have any problems with the new minimizer, please contact us immediately.
With a new load balancing framework and careful removal of serial bottlenecks, we have demonstrated scaling to 1024 or even 2048 processors on the ASCI Red machine. This work will be presented at SC2000 and is a finalist for the Gordon Bell award.