Ah, Ok. Sorry for this misunderstanding. I see what you mean now.
2013/8/2 Andreas Goetz <agoetz.sdsc.edu>
> This is not what I am talking about. I am referring to a switching
> function that interpolates forces on atoms between forces computed quantum
> mechanically and with molecular mechanics. This is not available in AMBER.
>
> The switching function that is implemented in AMBER and that you are
> referring to is for the cutoff of electrostatic interactions between QM and
> MM region under periodic boundary conditions. The short-range part is
> computed from the exact QM charge density while the long-range part is
> computed via PME using Mulliken charges.
>
> All the best,
> Andy
>
> --
> Dr. Andreas W. Goetz
> Assistant Project Scientist
> San Diego Supercomputer Center
> Tel : +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web : www.awgoetz.de
>
> On Aug 1, 2013, at 9:26 PM, Fabrício Bracht wrote:
>
> > What about using the switching function along the high collision
> frequency?
> > I saw that the the default for amber is to use the upper boundary for the
> > switch function is qmcut and the lower boundary is the high boundary
> minus
> > 2. Would it be possible to set the switch upper boundary to qmcut + 1 and
> > the lower boundary to qmcut -1?
> > Thank you
> > Fabrício
> >
> >
> > 2013/8/2 Andreas Goetz <agoetz.sdsc.edu>
> >
> >> Jason's interpretation is correct, the adaptive QM/MM code is currently
> >> available to developers collaborating with us. I had planned to release
> it
> >> with AMBER 12 but did not have time to properly test the code.
> >>
> >> I would strongly advice against using a step function at the QM/MM
> >> boundary. In the very least one should use a switching function for the
> >> forces as in Rode's "hot spot" method (Chem Phys 211, 1996, 313-323).
> >> Although it is possible to keep simulations somewhat under control with
> >> Langevin dynamics and a very high collision frequency (large value of
> >> gamma_ln) and still obtain structural properties (for example RDFs of
> ions
> >> in water) that are comparable to adQM/MM simulations with Bulo's DAS
> >> method. See for example my talk from the 2011 ACS spring meeting
> >> http://awgoetz.de/data/agoetz_adqmmm_acs-anaheim_2011.pdf (slides 18/19
> >> for step function, slides 28/29 for adQM/MM).
> >>
> >> All the best,
> >> Andy
> >>
> >> --
> >> Dr. Andreas W. Goetz
> >> Assistant Project Scientist
> >> San Diego Supercomputer Center
> >> Tel : +1-858-822-4771
> >> Email: agoetz.sdsc.edu
> >> Web : www.awgoetz.de
> >>
> >> On Jul 31, 2013, at 8:21 PM, Jason Swails wrote:
> >>
> >>> On Wed, Jul 31, 2013 at 3:05 PM, Fabrício Bracht <fabracht1.gmail.com
> >>> wrote:
> >>>
> >>>> HI Ross. I just read the paper describing the use adQM/MM in amber. It
> >> says
> >>>> there that the code has been implemented in amber, but you mentioned
> >>>> earlier that it will be a part of the next version of amber. I am
> >> guessing
> >>>> that the code that has been implemented is only available to
> developers,
> >>>> correct?
> >>>>
> >>>
> >>> The way I would interpret Ross's email is that adaptive QM/MM is only
> >>> developers. Variable solvent QM/MM is available in Amber 12.
> >>>
> >>>
> >>>> You also mentioned earlier the the discontinuity problems can be a
> >> problem
> >>>> if one does not use a very tight thermostat. By using langevin
> >> thermostat
> >>>> and a small gamma_ln value would I be able to use the adaptative
> scheme
> >>>> efficiently to include solvent effect on the qm region?
> >>>>
> >>>
> >>> The discontinuity is a problem of generic variable solvent -- a problem
> >>> that adaptive QM/MM solves by generating intermediate stages by which
> the
> >>> QM region is 'morphed' into MM continuously to avoid abrupt changes in
> >> the
> >>> potential that arises by swapping quantum water molecules. (At least
> >> that's
> >>> my understanding based on presentations I can remember).
> >>>
> >>> A small gamma_ln value would provide tighter temperature control and
> >>> _might_ stabilize vsolv=1 simulations. It may be worth trying.
> >>>
> >>> HTH,
> >>> Jason
> >>>
> >>> --
> >>> Jason M. Swails
> >>> BioMaPS,
> >>> Rutgers University
> >>> Postdoctoral Researcher
> >>> _______________________________________________
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> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
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Received on Fri Aug 02 2013 - 17:30:02 PDT
