[gmx-users] limit to the number of QM atoms in a QM/MM simulation?

[Kristina Woods]

Hi Benson,


> Cannot answer your question directly, but in addition to Orca, there is
> some effort in this area that may allow using software other than Orca
> for the QM part, for example:
> Zalevsky A.O., Reshetnikov R.V., Golovin A.V. (2019) New QM/MM
> Implementation of the MOPAC2012 in the GROMACS
> https://doi.org/10.1007/978-3-030-05807-4_24
>
> Benediktsson B. and Bjornsson R. (2017)
> QM/MM Study of the Nitrogenase MoFe Protein Resting State:
> Broken-Symmetry States, Protonation States, and QM Region Convergence in
> the FeMoco Active Site
> https://github.com/RagnarB83/chemshell-QMMM-protein-setup
>
>
> Olsen, Bolnykh, Meloni, Ippoliti, Bircher, Carloni and Rothlisberger (2019)
> MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry
> https://doi.org/10.1021/acs.jctc.9b00093
> http://manual.gromacs.org/2019/reference-manual/special/mimic-qmmm.html
> (I belive this is still in progress
>
>
Thank you for the reply and for the information.  I have not tried using
the new implementation of gromacs with MOPAC2012 but I will certainly look
into it.  I have looked into the MiMiC implementation (using CPMD) and it
is apparently not quite ready for use.  My feeling is that my issue is with
gromacs and not with ORCA.  If I remove the protein and just do a QM
simulation with the QM atoms in ORCA there is no problem.  Before I scrap
everything and move on I would like to make sure that I am not just missing
something very obvious that may be  easy to fix.

Thank you,
Kristina


> > Hello:
> >
> > I have a very basic question about the QM/MM implementation in gromacs
> (and
> > yes - I know that it is no longer supported).  I am using ORCA as the
> > quantum chemistry package for a QM/MM simulation of a photo-protein in
> > gromacs.  I have successfully used the combination of ORCA and gromacs
> with
> > other photo-protein QM/MM simulations without problem but in the previous
> > cases I have had a smaller number of QM atoms (below 200 atoms).  In my
> > current protein, I would like to consider close to 700 atoms but I notice
> > that everytime I set-up a simulation in gromacs - gromacs fragments the
> > geometry of the system so that only a limited number of the QM atoms are
> > contained within the simulation box.  The rest of the atoms are
> translated
> > out of the simulation box (sorry if this is not a good description).  I
> > have tried compiling different combinations of gromacs and orca and this
> > doesn't seem to change anything.  I have also studied the input geometry
> of
> > my system and that seems to be fine (the initial geometry comes from the
> > output of a 100 ns all-atom MM simulation of the entire system).  I then
> > tried to simulate only of a subset of the QM atoms (up to 200 atoms) of
> > interest and with a smaller system everything seems to work beautifully.
> > So my question is if my problems are attributed to the fact that there
> is a
> > limit to the number of QM atoms that can be considered in a QM/MM
> > simulation?
> >
> >
> > Thank you,
> >
> > Kristina
>
>
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