On Tue, Jul 30, 2013 at 3:27 PM, Fabrício Bracht <fabracht1.gmail.com>wrote:
> Can a distance based mask be used to specify atoms in the qm region of
> qm/mm simulations?
Yes it can. But it is worth noting that, in most cases that I'm aware of
where masks are used in Amber, the atom selections are fixed after the mask
is initially evaluated. That is, the mask is not dynamically updated as
the coordinates change (this is true in cpptraj as well).
> If not, is there a practical way to work around the
> diffusion of water molecules out of the qm region.
>
I believe what you're looking for is 'variable solvent' or 'adaptive QM/MM'
(the latter is a generalization of the former, as far as I know). To my
knowledge, this method is not documented in either the Amber12 or
AmberTools 13 manuals (or if it is, I could not find it).
The best source of information pertaining to running these simulations will
come from the test cases ($AMBERHOME/test/qmmm2/variable_solvent/). I
think I was able to get a general idea about running these calculations
from quickly glancing at both the input and output files in that test
directory (e.g., nearest_qm_solvent=8 means include the 8 nearest water
molecules and nearest_qm_solvent_fq=2 means update the quantum region every
2 steps). I would also suggest setting debug=1 in the &vsolv namelist to
trigger more printout when you are first learning how to use this method.
[You could always take a gander at the source code, too.]
Perhaps someone with more knowledge of this code can chime in with more
complete instruction, but this is hopefully enough to get you started.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 30 2013 - 20:30:02 PDT
