[gmx-users] QM/MM simulations (Mark Abraham)

Groenhof, Gerrit ggroenh at gwdg.de
Tue Aug 30 08:04:04 CEST 2016


Unless there are no atoms in the QM region, the QM energy should not be zero. 

Can you confirm that mdrun writes an input file (input.com)? and gaussian is executed?

If not, has gromacs been compiled with QMMM support (GMX_QMMM_PROGRAM:STRING=gaussian)?




Sadly, most of the QM/MM interfaces have been lacking a maintainer on the
GROMACS side for quite a number of years. You should definitely be
following http://wwwuser.gwdg.de/~ggroenh/qmmm.html closely.


On Mon, Aug 29, 2016 at 9:36 PM Clinton King <clintonking36 at chem.byu.edu>

> I'm performing a QM/MM (using Gaussian 09 and Gromacs 5.1.2) simulation of
> a single molecule of octanol in a box of water. In examining the standard
> output, it appears that call to Gaussian is proceeding as expected, but
> looking at the log file, it doesn't appear that quantum energy is being
> communicated correctly, ie the output looks like the following:
>            Step           Time         Lambda
>            7000        7.00000        0.00000
>    Energies (kJ/mol)
>         LJ (SR)          Disper. corr.       Coulomb (SR)   Coul. recip.
>      Quantum En.
>     2.45033e+04   -1.74106e+02   -1.86935e+05    6.68753e+01    0.00000e+00
>       Potential          Kinetic En.         Total Energy    Temperature
>      Pres. DC (bar)
>    -1.62539e+05    3.00966e+04   -1.32443e+05    2.97582e+02   -2.34549e+01
>  Pressure (bar)   Constr. rmsd
>    -7.37300e+01    8.07450e-06
> Notice that the entry for Quantum En. is 0.000.
> Has anyone else seen this problem before? If so, what did you do about it?
> --
> Clinton King
> Graduate Student
> Chemistry Department
> Brigham Young University
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