AMBER Archive (2009)

Subject: [AMBER] RE: Questions about QMMM

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jul 21 2009 - 17:47:49 CDT

Hi Hong,

 

It is best to post such questions to the AMBER mailing list in future so
that others can benefit from the replies as well. See
http://lists.ambermd.org/ for signup details.

 

In AMBER it is certainly possible to have MM atoms, such as waters, situated
between QM regions. However, the only downside at the moment is that there
is no partitioning of the two QM regions. Thus they will be treated as a
single QM region with a single fock matrix, single SCF etc. This is fine in
principle with respect to the results but means you don't get any speed
advantage from having two separated QM regions. That said in your case I
think what you would get is actually what you want since you want these two
QM regions to approach each other yes?

 

You should be able to just setup your simulation and as the two regions
approach so the two QM regions should essentially coalesce without any user
intervention. Thus set this up just like you would a normal (single region)
QM/MM simulation and you should be good.

 

Good luck,

Ross

 

From: hong-bin Xie [mailto:xhbxhb1980224_at_gmail.com]
Sent: Tuesday, July 21, 2009 8:56 AM
To: ross_at_rosswalker.co.uk
Subject: Questions about QMMM

 

Dear Dr Walker:

  Sorry to trouble you with question about QM/MM in Amber.

It is well known that system that will be calculated by QM/MM potential is
partitioned into two regions: a QM region and MM region.

Always, I found that MM region just surrounds QM region. I want to know
whether MM region may lie between two QM parts. For example: I study the

reaction between two molecules A and B in aqueous solution. Surely, in the
process of simulation, A and B are defined as QM region, and waters are

defined as MM region. I want to know whether waters in MM part can be
possibly put in the position between A and B in the process of simulation?

That is to say, I want to consider the influence of water shell on the
reaction when B attack A. Is it possible?

Any help would be appreciated. 

-- 
Best Wishes
Sincerely Yours
Hong-bin Xie
---------------------------------------------------------------
Hong-bin Xie
Postdoctoral Researcher
Department of Chemical Engineering
University of Pittsburgh
Email:xhbxhb1980224_at_gmail.com <mailto:Email%3Axhbxhb1980224_at_gmail.com> 

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber