Subject: CCL: Summary) Amber is MM or MD?

From: "Telkuni" <telkuni:at:venus.dti.ne.jp>
Date: Thu, 4 Dec 2003 11:30:08 +0900

Hello, CCLers.

I've asked the classification and nature of Amber as written in title.

--- original question ---
> Although I think it is very basic knowledge, I want to know the truth.
> 
> Some papers and books treat AMBER as Molecular Mechanic method 
> describing with force fields and bonding parameters. But others treat 
> AMBER as Molecular Dynamic method describing with potential functions.
> 
> Does AMBER belong MM or MD? and or both of them?
> 
> >...All responses, I will appreciate. And I will summarize them.

Here is the summary. Thank you very much for the people who sent 
me the replies.

1) from Konrad Hinsen  ---------------------

Both. MM refers to the kind of model that is used to describe the chemical 
system, MD to a particular simulation method.

2) from David F. Green ---------------------

Telkuni,

Molecular Mechanics is a term used to describe a type of model for
molecular systems.  In a Molecular Mechanics model (sometimes also
referred to as an Emprical Force Field model), the molecular properties
are treated by terms derived from macroscopic physics.  For example, bond
terms may be treated as a harmonics oscillator, electrostatic interactions
may be treated by Coulomb's Law, and so on.  In this sense, Molecular
Mechanics is a term which differeniates a model from Quantum Mechanics 
(including ab initio and semi-empirical models), where the underlying
description of a molecule is based on microscopic physics (i.e. quantum
mechanics).

Molecular Dynamics, on the other hand, describes a similuation technique,
in which Newton's Laws of motion are propogated over an energy
surface.  Thus MD should be used to differentiate from other techniques
for conformational sampling over an energy surface (such as Monte Carlo).
MD can be employed using a Molecular Mechanics force field, or a Quantum
Mechanical description of the energetics, just as MC methods can.  

AMBER includes a Molecular Mechanics force field designed primarily for
simulation of biomolecules, comparable in structure, but differing in
details from the other biomolecular force fields such as CHARMM,
OPLS, or GROMOS, and perhaps varying a little more from MM force fields
designed for simulation of other molecules (such as MM3).  In addition,
AMBER provides a set of code for preforming many types of simulations,
including MD.  Again, many other packages implement many of the same
features, including CHARMM, GROMACS, NAMD, and many more.  There are
really three independent portions to molecular simulations: (1) the force
field, (2) the simulation method, (3) and the software 
implementation.  The confusion arises in that the software package name is
often also used for the force field name, particular in the case of AMBER
and CHARMM.  

I hope this clears some things up.

David

** And, I've copyed here Dr.Feenstra's CCL-mail answring the question of 
Dr.Tamulis, becouse it is concerning my questuion.
> Dear Prof. Telkuni Tsuru and other Netters,
> 
> I am working with quantum mechanical Hartree-Fock and Density Functional
> Methods. Would you be so kind and explane me more detail what it is the
> difference between methods:
> 1) MM, describing with force fields and bonding parameters and
> 2) MD, describing with potential functions ?

In the terms you use, there is no difference. Both use *potential functions*
to describe *bonding paramaters*, together these are called a *force field*.

One can view Molecular *Dynamics* as a special case of Molecular *Mechanics*
where dynamics comes in through assigning velocities to all atoms (and hence
a system *temperature*), and integrating the (Newtons) equations of *motion*.

> Which is more exact in comparison with quantum mechanical methods?

IMHO, that is not a sensible question. The realm, if you will, of both methods
(i.e. 'QM' vs 'MM/MD') and possible applications, is so different that there
is no sensible way in which to compare them. Furthermore, many parameters in
the forcefields have their basis in QM calculations, so that MM/MD can be said
to be derived from QM, which implies it is less accurate. But on the other
hand, the MM/MD parameters are also based on (other) experimental knowledge
(often thermodynamical parameters like heat of vaporization) which make them
on a certain level of application at least in principle more correct (and
at the same time they are, obviously, empyrical parameters with limited
applicability).

4) from  ---------------------

5) from  ---------------------

6) from  ---------------------