FYI - Adaptive QM/MM support will be part of the next version of AMBER. It
would have been available earlier but unfortunately NSF ran out of money
before they could fund our proposal for developing the method further.
All the best
Ross
On 7/30/13 8:15 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
>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
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 30 2013 - 20:30:03 PDT
