From owner-chemistry@ccl.net Tue May  9 12:31:00 2006
From: "Ross Walker ross_-_rosswalker.co.uk" <owner-chemistry~~server.ccl.net>
To: CCL
Subject: CCL: Combined Molecular Dynamics and Semiempirical Methods
Message-Id: <-31723-060509121231-15848-Resn48DJ0cTAGIuSoT3MXg~~server.ccl.net>
X-Original-From: "Ross Walker" <ross:rosswalker.co.uk>
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Date: Tue, 9 May 2006 09:12:17 -0700
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Sent to CCL by: "Ross Walker" [ross .. rosswalker.co.uk]
Dear Heribert,

> I'm looking for a way to do a classical molecular dynamics simulation 
> of a liquid (ideally with a polarizable Force Field), but with one 
> molecule treated by semiempirical methods (PM3 or similar), so 
> basically a QM/MM calculation. I know that there is the GAMESS-Tinker 
> combination, but it seems that it does not allow to compute 
> trajectories (also the version of Tinker used seems to be a bit old). 
> 
> Anyone knows a possibility to do this? A bit of additional 
> programming 
> would not be an unsurmountable hurdle. 

Amber 9 has full support for QM/MM MD simulations that can combine a number
of different semi-empirical Hamiltonians with any of the Amber force fields.
It also supports a full treatment of long range electrostatics using a
Particle Mesh Ewald approach for the QM/MM calculation and also supports
QM/MM with Generalized Born implicit solvent. The implementation is also
very simple so that if you have a simulation setup to run classically in
Amber already you only need to change a couple of entires in your input file
and you are good to go.

Details on amber are at http://amber.scripps.edu

A tutorial on AMBER 9 QM/MM is at
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_Six_amber9/ind
ex.htm

All the best
Ross

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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
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