Thank you very much Jason and Ross for the reply.
Any idea to when the next version of amber is coming out?
Thank you
Fabrício
Em 31/07/2013 00:24, "Ross Walker" <ross.rosswalker.co.uk> escreveu:
>
> 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
> >_______________________________________________
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> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Tue Jul 30 2013 - 21:00:04 PDT
