NAMD should be able to run on all flavors of Windows(NT, 2000, XP, etc). One can even run NAMD on a cluster mixed with Windows and Linux i386.

There are two versions of NAMD that can run on Windows:

1. Win32-i686-MSVC of NAMD with net-win32 of Charm++

2. Cygwin-i686 of NAMD with net-cygwin of Charm++

Four ways of running NAMD on Windows:

1. parallel run with ssh on Cygwin (Cygwin-i686 only)

install Cygwin (free from http://www.cygwin.com/ ), with openssh installed and 

configured. After this, one can start a bash window running ssh daemon, and make it totally a Linux like box.

2. parallel run with charmd.exe:

Charm++ comes with a charmd (Charm daemon) utility program for Windows in the 

binary distribution. Run the Charm daemon on every processor, and then one can start a parallel job using charmrun.exe.

3. sequential run:

One can directly run namd2.exe with simulation config file on his/her desktop/laptop.

4. parallel run on a single SMP machine:

One can also choose to run multiple copies of namd2.exe on a single machine:
  ./charmrun +p2 ./namd2.exe some.conf  ++local