[gmx-users] gromacs QMMM gaussian 09 (g09) input format

Gerrit Groenhof ggroenh at gwdg.de
Wed Jan 21 15:03:26 CET 2015


Not sure if you're still interested in pursuing this further.

All units are atomic units, and upon reading the gradients (in au), gromacs converts these again.

You mentioned it was running with gaussian, from which I infer you have re-compiled the links that required modification. However, from what your wrote at the end of your email, it seems that gaussian was not modified. My guess is that this is the reason why your simulations crash.

For gromacs version < 5.0 one may also avoid hacking the gaussian source code by calling a wrapper script instead of the gaussian binary, provided gaussian09 is installed and working correclty on your system. For details and the script: http://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian



Dear gromacs users/authors
I'm trying to run gromacs with QMMM support (so far I tried
g09,orca,mopac) and the best I could do is run test simmulation (spc
water box, 213 molecules) only with g09 (gromacs with mopac support
fails to compile, test simulation with orca fails with seg. fault after
orca finishes calculation but it is possible that my settings for orca
are bad, i tried orca only now).
	Unfortunately, this simulation is unstable - QM atoms moves too fast
and (eventually, after some time calculation crashes because gromacs
sends to gaussian molecule with atoms that are 10nm away from each
other). For me it looks like gradients read from fort.7 are in different
units/ are something completely different than gromacs expects. 
Could you please help me where I can find what format (units, what
interactions needs to be included) gromacs expects from gaussian? It is
not obvious for me from gromacs source code. 
Or maybe if you could help me how to modify gaussian source code? (i saw
roadmap.pdf but this is for g03 and I can't find lot of those
functions/equations in g09, therefore I didn't try to change those I
could find in g09 yet. Also I tried to compile g03 with gfortran but
without any luck)

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