Re: [AMBER] Distance based mask for qmmask

From: Jason Swails <>
Date: Wed, 31 Jul 2013 23:21:41 -0400

On Wed, Jul 31, 2013 at 3:05 PM, Fabrício Bracht <>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.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jul 31 2013 - 20:30:04 PDT
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