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

[Kristina Woods]

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

There is a 1.2 nm shell of solvent around the protein.  I for some reason
didn't really consider that this could be a PBC visualization issue - but
this would make a lot of sense.   I will try to figure out if this is the
problem.  Thanks for the suggestion!

K

>
>
>
> > 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
> http://www.thelemkullab.com
>
> ==================================================
>
>
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