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
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>>AMBER.ambermd.org
>>http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Tue Jul 30 2013 - 21:00:06 PDT
