Re: [AMBER] Distance based mask for qmmask

From: Ross Walker <>
Date: Tue, 30 Jul 2013 20:42:13 -0700

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.


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

On 7/30/13 8:30 PM, "Jason Swails" <> wrote:

>On Tue, Jul 30, 2013 at 11:22 PM, Ross Walker <>
>> FYI - Adaptive QM/MM support will be part of the next version of AMBER.
>> 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.
>Jason M. Swails
>Rutgers University
>Postdoctoral Researcher
>AMBER mailing list

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Received on Tue Jul 30 2013 - 21:00:05 PDT
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