AMBER Archive (2009)

Subject: Re: [AMBER] the criterion of equilibrium

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Sat Oct 24 2009 - 13:22:25 CDT

My three cent's of opinions worth for today.
I insist that we stop talking about equilibrium, when we clearly mean
'relaxation'.

Equilibrium, or equilibrated simulations are of course impossible to
achieve. They would have to run for exactly: forever.

What we might to know is, if we keep running will the answer change ?
Again, tricky, tricky question. Of course it will change!

Current ideas tells you that you should run multiple simulations for
quite a bit of time, and compare those answers.

Now, for relaxation runs, one should NOT even look a the answers until
the important properties have 'stabilized', by which I mean plateaued.

Look at the density if using NPT, NOT at the pressure (which fluctuates
a lot).

The fluctuations in the total energy should be roughly the same as those
for potential energy.

The RMS vs the original structure should be more or less becoming
constant. This is not as trivial as it looks. If you start from a
structure very different from your final result, the RMSD will indeed
look constant but that is a simple artifact of the behavior of RMSD when
structures are very different from each other.

If teh RMSD becomes 'stable' at values smaller than 4 or 5, them it is
ok to think of the system as relaxed.

Cheers

Adrian

Bill Ross wrote:
>> I want to know the criterion of equilibrium of molecular dynamics, when
>> analysize the summary.ETOT, what can be called the system has equilibrated,
>> in other words, how much the energy can diviate from the average?
>
> I think the thing to watch is not so much the short-term fluctuations,
> but rather the long-term trends of various quantities, to see if they
> have leveled off.
>
> Bill
>
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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu

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