Dear Lehtola and GMX users:

Thanks a lot for your comments on re-autoconf.
I'd tried a few but finally found that  was not necessary.
I'd obtained shared gromacs-3.3.3 binary on CYGWIN just
add -no-undefined option (needed to obtain DLL on CYGWIN) 
for linkage of cyggmx-4.dll with libtool in src/gmxlib/Makefile.in 
and then compiled with
./configure --without-x --with-fft=fftpack --enable-shared
(--disable-float).
The above also works for the shared binary build with MinGW32.

Kind Regards.

Makoto Yoneya, Dr.
AIST, Japan

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