AMBER Archive (2009)

Subject: RE: [AMBER] QM/MM types.

From: Ross Walker (
Date: Thu Aug 13 2009 - 11:11:57 CDT

Hi Rodrigo,

> I was wondering.
> What are the main differences between the QM/MM methods
> found in AMBER, Q-Chem, Car-Parinello and (not being exactly the same)
> Gaussian's ONIOM?
> When you should use one or the other?

This is an extremely complicated question that cannot really be asked in a
forum such as this. I would suggest starting with the basic theory of QM and
QM/MM. Take a look at some of the text books on QM methods. You also need to
consider the differences between optimizations and MD. The key differences

1) AMBER = designed for MD (Newtonian). QM/MM is semi-empirical internally
and optimized for MD simulations. Hooks to ab initio packages is possible
through pupil.

2) Car-Parrinello = ab initio first principles MD. DFT based.

3) Q-Chem = Ab initio MD package - generally for optimization of systems.
May be able to do semi-empirical.

4) Gaussian Oniom method = a way of doing optimizations with different
levels of theory. Be aware DO NOT use the AMBER force field in Gaussian!!!
It is crazy old and very broken!

The main point is that if you do not know the differences between classical
MD, Born-Oppenheimer dynamics vs first principles MD. And what DFT, Ab
initio, semi-empirical etc mean then you need to learn this theory before it
is possible for someone to give you an understandable answer to your
question I think.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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