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

[Kristina Woods]

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