1. Download cygwin from http://www.cygwin.com/
a. click on the link to "install from internet" and run the installer
b. when you get the dialog that asks you what packages to install expand and select "gdn" "gdb" and "make"
c. follow the rest of the installation instructions
EDIT: this website has a pictorial guide to install the packages with cygwin. I forgot to mention they are all under Developer, so expand that first.
EDIT: also install the tcsh package
2. Next you are going to need the GROMACS source code. You can get it here.
a. download and save the file someplace handy
3. Next you need FFTW. There are pre-compiled dlls for Windows, but I would recommend not using them unless you know how to set the path variables. The easiest way is to grab fftw-3.2.1.tar.gz . Again, save this someplace handy.
4. create a folder someplace (C:\FFTW) and extract FFTW to it.
5. start cygwin and change the directory to your FFTW folder: cd c:\fftw
6. type: ./configure --enable-threads --enable-sse --enable-float
7. then: make
8. then: make install
9. now create a folder for gromacs (C:\gromacs) and extract the distribution there. There should be a few folders like admin, src, etc.
10. in the cygwin console, change your directory to the gromacs folder: cd c:\gromacs
11. type: ./configure --enable-shared LDFLAGS='-L/usr/local/lib'
12. then: make (this took a couple of hours to run through)
13. then: make install
14. make links
15. make clean
when you get your prompt back in cygwin (or from a fresh session change your directory to c:\gromacs) type: luck
to test if you have access to gromacs. You should get something like:
gcq#93: "Pretend That You're Hercule Poirot" (TeX)
Also note I really haven't tested anything else yet, so this could all end up to be bogus. However if you're not really a computer guy, all bringing your ibook to dinner "in case you need to compile something" like me, then you may find this a good start. I'll update as necessary.
P.S. I like 7-zip for all my extracting needs. Let me know of any problems or mistakes with the above.