The directory tree for the build is as follows:
Top_level
|
+-dist (a directory to hold the compiled gromacs binary tree:
|       ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.2.tar.gz)
|
+-mcpp (mcpp binary distribution which can be gotten from: 
        http://mcpp.sourceforge.net/download.html

ReadMe.html,License.txt and GMX_installer.nsi should all reside in the top level directory



--==compiling gromacs from original sources==--

- Untar the sources into a temporary directory.

- Make the following modifications:
  * comment out the eof() function in include/futil.h and src/gmxlib/futil.c
  * add #undef HAVE_UNISTD_H right before #ifdef HAVE_UNISTD_H in src/gmxlib/statutil.c,main.c
  * comment out blocks and lines with SIGUSR1 references in src/kernal/md.c

- re-make the tar as gromacs-3.3.3-modified.tar.gz

- copy that tar file into C:\modified_sources

- You are now ready to run the build script located in the packaging directory