We don't really support windows, but we do try to keep the code portable even if we don't check every version on Windows. In practice that means there might be bugs in a new release that prevents it from compiling, but it should be easy to fix.

The easy way is to use Cygwin from http://www.cygwin.com/. With cygwin you can compile Gromacs just as you do in Unix, and you will be able to run X-windows and Xmgr.

If you want a native version you'll have to live without ngmx and other things that depend on X-windows. Download the latest stable source and unpack it. Then download the precompiled FFTW libraries from ftp://ftp.gromacs.org/pub/developer (you do not need the development part of FFTW). Read the README file and install them.

Then you should download the Microsoft Visual C build environment for Gromacs. You can find it as gromacs_win32dev.zip in the developer directory on the ftp site. Unpack that file in the Gromacs source directory so you have a win32 subdirectory. Copy src/config.win to src/config.h and open the build workspace in win32/gromacs inside Visual C. Select Debug or Release, and finally build the "all gromacs programs" target to build all programs, or just "mdrun". Dependencies will be built automatically.

But once again - please note that Windows is not a supported platform. We'll be happy to include your fixes, though :-)