[gmx-users] QMMM free energy

David Mobley dmobley at gmail.com
Tue May 29 23:42:17 CEST 2007


I haven't heard of anyone who has done this in GROMACS yet. My hunch
is it will require some changes. Stay tuned to hear from the


On 5/29/07, Robert fiske <rfiske_ at hotmail.com> wrote:
> I am looking to do QM/MM free energy calculations, first I am running tests
> with the free energy tutorial by David Mobley.  I have matched his results
> using a pure MM free energy run, and am now looking to move to the QM/MM
> step.
> I added the methane molecule as my quantum system and tried running the
> first lambda.  At the steep minimization step however I get a bus error,
> using gdb it comes from nslist being 0 in new_i_nblist, the error occurs in
> the call from ns.c:979.
> Looking at the code it seems that the quantum case is taken care of inside
> the condition of "!bFreeEnergy"  Inside the provided bQMM case only the coul
> pointer is passed to the function that fails, however vdwc is passed in the
> free energy code (which is set to NULL earlier in the code). So my question
> is:
> Is QM/MM free energy calculation possible in the current version of gromacs
> (3.3.1 modified to work with CPMD is what I'm trying), or is there a
> parameter option to fix this type of issue?
> Thank you for any help you can provide
> Robert Fiske
> Gogonea Group
> Cleveland State University
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