Re: [AMBER] Distance based mask for qmmask

From: Andreas Goetz <agoetz.sdsc.edu>
Date: Thu, 1 Aug 2013 20:34:15 -0700

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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 01 2013 - 21:00:02 PDT
Custom Search