Re: AMBER: On the temperature increasement in the restriction MD in the tutorial 2 section 5

From: Thomas Cheatham <>
Date: Wed, 13 Sep 2006 09:48:54 -0600 (Mountain Daylight Time)

> For
> I have a question on the temperature increasement.
> First of all, for initial temperature 0 K, it cannot
> reflet the real system, because a real system can
> never has a frozen temperature. Is the parameter
> initial T=0 correct or not?

Please read the manual; if TEMPI = 0, the initial forces are used.
If the system is appropriately minimized prior to MD, this is OK. If not,
then this is ill-advised as the initial forces could be large and lead to
instability. Setting TEMPI=10.0 is probably wiser.

However, there is nothing wrong with having a TEMPI close to zero; a real
system can get close to zero. A Google search shows that in 2003 a MIT
group cooled sodium gas to half a billion'th of a degree above absolute

Temperature is also somewhat artificial in the MD world; it is simply a
measure preportional to the mean-squared velocity of the atoms in the
system. Any reality of the defined temperature, in comparison with
experiment, depends on the underlying potential/forces and masses.

> Secondly, for this md, the total length will be 20 ps.
> How long does it to take to increase the temperature
> from 0K to 300K?

This will of course depend on the temperature coupling algorithm (if
applied) and associated parameters. The best way to answer your question
would be to experiment. Running a 20 ps simulation on a laptop is
straightforward. Playing with the parameters and seeing what occurs (for
example GB compared to explicit water, various temperature couplings,
pressure changes, time steps, ...) will tell you much more than what you
can learn by reading responses to the e-mail reflector and also give you
experience in how to interpret what sander/AMBER dumps out.


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Received on Sun Sep 17 2006 - 06:07:06 PDT
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