

When using CHARMM or AMBER for molecular dynamics, the system is usually
heated to the required temperature, ran in an equilibration period, and
only then is the actual production run.  However, in Discover, there is
no heating phase.  The system is instanteously heated to the required
temperature and equilibrated before the production phase.

Why the difference in the two approaches?  What is Discover doing
differently from CHARMM and AMBER so that a heating phase is not
required?

========================================================================

Basically, it appears that the difference lies merely in a
philosophical difference in running molecular dynamics simulations.
The folks at Biosym (now MSI) felt that instantaneous heating was
acceptable if the equilibration period was handled correctly.  However,
the authors for CHARMM and AMBER felt that a heating period was
necessary at all times.

Here are edited excerpts from the few responses that I got.  If anyone
has some references with some hardcore data, I'd appreciate hearing from
you.

From: [email-masked] (Randy Zauhar)

       This is a question of "computing philosophy"...
       What is the benefit of slow heating? I have seen some argue that
overall equilibration time is improved if you use slow heating, rather
than "jarring" the system by rapidly increasing the temperature. In my
very subjective evaluation, it probably doesn't matter that much. 
     ...the algorithms are indeed different. In the heating method,
  atom velocities are simply rescaled at set intervals of dynamics
steps.  In the heat bath method, atomic velocities are rescaled at every
step with the velocity scaling controlled by factor whose functional
form includes the ratio of current to target temperature, as well as a
temperature coupling factor that controls how rapidly the temperature is
adjusted toward the target value.

From: [email-masked] (Peter Slickers)

In me opinion it depends on the system you are modelling and not 
on the software whether an extended heating and equilibration phase 
is requiered. I have run some MD simulations with DNA in a box of 
water with counterions and salt with AMBER 4.1. For such a system 
with several mobile charges you need a carefull and extended 
heating procedure, otherwise the DNA double helix will disrupt. 

From: Leif Laaksonen <[email-masked]>

I'm not sure but I see this as a semantic issue. Combining the heating
and equilibration into one stage should be no problem. You can more or
less assign the atom velocities and scale them directly. I guess CHARMM
has an explicit heating stage to prevent "shock" heating by allowing the
user to control the speed in which the temperature is raised. 

-- 
						Jeff Nauss

***********************************************************************
*  UU    UU             Jeffrey L. Nauss, PhD                         *
*  UU    UU             Director, Molecular Modeling Services         *
*  UU    UU             Department of Chemistry                       *
*  UU    UU CCCCCCC     University of Cincinnati                      *
*   UU  UU CCCCCCCC     Cincinnati, OH 45221-0172                     *
*    UUUU CC                                                          *
*         CC            Telephone: 513-556-0148    Fax: 513-556-9239  *
*         CC                                                          *
*          CCCCCCCC     e-mail: [email-masked]                  *
*           CCCCCCC     URL  http://www.che.uc.edu/~nauss             *
***********************************************************************