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

Justin Lemkul jalemkul at vt.edu
Tue Sep 3 16:21:49 CEST 2019

On 9/3/19 3:42 AM, Kristina Woods wrote:
> 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

How large is the buffer of of solvent around the protein? This sounds 
like a simple PBC visualization issue.


> 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


Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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