NAMD Wiki: NamdOnWindows
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