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?
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?
Thank you
Fabrício
2013/7/31 Ross Walker <ross.rosswalker.co.uk>
> Here's the official JCTC links for the two papers for those that are
> interested:
>
>
> http://pubs.acs.org/doi/abs/10.1021/ct300331f
>
> and
>
> http://pubs.acs.org/doi/abs/10.1021/ct900148e?journalCode=jctcce&quickLinkV
> olume=5&quickLinkPage=2212&selectedTab=citation&volume=5
>
> All the best
> Ross
>
> On 7/30/13 8:42 PM, "Ross Walker" <ross.rosswalker.co.uk> wrote:
>
> >Yes it is there but it is:
> >
> >1) Only for waters
> >
> >2) Uses a hard cutoff at the QM/MM boundary - I.e. as a water leaves and a
> >new water enters there is no accounting for this not being a smooth
> >transition. This leads to discontinuities in the potential and hence
> >instability unless a very tight thermostat is used. The best option is to
> >use a proper transition region based adaptive approach that gives smooth
> >potentials as a water molecule transitions from QM to MM.
> >
> >See: http://www.rosswalker.co.uk/papers/ct300331f.pdf
> >
> >as well as
> >
> >JCTC 2009, 5, 2212
> >
> >And the AMBER adaptive QM/MM paper that should have been written by now
> >(hint hint - names with-held to protect the guilty).
> >
> >All the best
> >Ross
> >
> >
> >
> >On 7/30/13 8:30 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
> >
> >>On Tue, Jul 30, 2013 at 11:22 PM, Ross Walker <ross.rosswalker.co.uk>
> >>wrote:
> >>
> >>>
> >>> 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.
> >>>
> >>
> >>But "variable solvent" is there, right? It appears to have a test case
> >>in
> >>Amber 12, and I couldn't find any reason why the code would trap it...
> >>
> >>If all you need to do is swap solvent, you may be able to get away with
> >>vsolv=1, but I'll defer to the experts on this one.
> >>
> >>HTH,
> >>Jason
> >>
> >>--
> >>Jason M. Swails
> >>BioMaPS,
> >>Rutgers University
> >>Postdoctoral Researcher
> >>_______________________________________________
> >>AMBER mailing list
> >>AMBER.ambermd.org
> >>http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> >_______________________________________________
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> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Wed Jul 31 2013 - 12:30:02 PDT
