[gmx-users] Configuring QM/MM for Gaussian/GROMACS

[Michael Eby]

Hi,

I've been trying for days to try to figure out how to configure GROMACS
for mixed QM/MM modeling, and it is a nightmare. The only manuals in
existence seem to give less than half the story, and I have no
experience with this kind of program.

I have managed to do ./configure --with-qmmm-gaussian, make, make
install, although I was unable to get MPI or FFTw working. I then
extracted the Fortran subroutines listed in
http://wwwuser.gwdg.de/%7Eggroenh/roadmap.pdf, although most of the
subroutines supposedly in l701.F were actually in osutil.F or utilam.F,
and I'm not sure I added coding in the right place, if that matters,
since the pdf doesn't indicate where to add it. I decided to add it at
the bottom of the coding, but before the RETURN and END commands. I have
also created a subdirectory ~/modlinks/ which contains l301, l510, l701,
and l9999 directories.

My problem now is attempting to make the executables (l301.exe,
l510.exe, l701.exe, and l9999.exe). Apparently I need make files similar
to http://wwwuser.gwdg.de/%7Eggroenh/l301.make, but I cannot figure out
how to write them or where to find them. Even with this make file, I
still don't understand how to actually build the executable.

Finally, I will need to change several environment variables to set the
path of ~/modlinks, but I'm not sure which ones. The manual seems to
indicate inserting %subst lxxx /home/user/modlinks/lxxx (where lxxx is
presumably l301, l510, l701, or l9999) into the input file (but it
doesn't say which input file, when, or where), and setting $DEVEL_DIR to
~/modlinks, but again, not how to do this.

Any help here would be greatly appreciated. I really don't have any idea
what to do, and there seem to be literally no web sites (at least none
found by Google) with any advice whatsoever.


My setup:
GROMACS 4.0.5, single precision
Gaussian g03
OS: Ubuntu
shell: bash


Thanks


Michael Eby