Re: A question of time

From: David A. Case <>
Date: Tue, 10 Jun 2003 09:34:19 -0700

On Tue, Jun 10, 2003, Darren Davies wrote:
> I am rather new to AMBER and molecular dynamics and
> was wondering how accurate the timestep used in AMBER
> is.
> If you carry out a 1 ns simulation, does this really
> represent 1 ns in the real world? If not, how accurate
> is simulated time? Are there any papers you can
> recommend on this subject.

It's not quite clear what you are asking.

The *precision* of the time is primarily limited by the fact that atomic
masses are entered into the program to only about four or five significant
figures; this implies that the time scale is accurate to about one part in
ten thousand. If you need more precision, you have to think hard about
questions of isotopic abundance, etc.

The *accuracy* of the time course is primarily limited by the force fields.
For example, the viscosity of TIP3P water is lower than that of real water,
so that water molecules will rotate and translate more quickly than they
should. This can lead to large discrepancies with the "real world". You
might look at:

%A P. Mark
%A L. Nilsson
%T Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K
%J J. Phys. Chem. A
%V 105
%P 9954-9960
%D 2001


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Tue Jun 10 2003 - 17:53:00 PDT
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