Re: AMBER: Temp control

From: David A. Case <>
Date: Fri, 13 Aug 2004 13:13:20 -0700

On Fri, Aug 13, 2004, ding wrote:
> We want to do MD simulation in explicit water and free energy calculation
> for DNA system. We did notice that the langevin dynamics (ntt=3) is used to
> control the temperature in Amber tutorial. Has anyone tested this new method
> in simulations? How does it work in temperature control compare to ntt=1?

The Berendsen thermostat (ntt=1) has the advantage that it provides only a
mild perturbation on the dynamical properties of the system; see, for example:

%A A. Mudi
%A C. Chakravarty
%T Effect of the Berendsen thermostat on the dynamical properties of water
%J Mol. Phys.
%V 102
%P 681-685
%D 2004

But it has some potential (and real) disadvantages. It does not sample a
true canonical distribution, but a slightly different ensemble:

%A T. Morishita
%T Fluctuation formulas in molecular-dynamics simulations with the weak
coupling heat bath
%J J. Chem. Phys.
%V 113
%P 2976
%D 2000

Also, it can have pathological effects, most of which Amber will avoid, but
you should still be careful:

%A S.C. Harvey
%A R.K. Tan
%A T.E. Cheatham, III
%T The Flying Ice Cube: Velocity Rescaling in Molecular Dynamics Leads to
Violation of Energy Equipartition.
%J J. Comput. Chem.
%V 19
%P 726-740
%D 1998

The Berendsen heat bath is especially poor for implicit solvation, since it
can do a poor job of temperature regulation when there is no explcit solvent.

Langevin dynamics can be used for both implicit and explicit solvation. It
does a good job of (relatively quickly) sampling a canonical distribution, and
seems to be very robust. The main drawback is that is perturbs the dynamical
behavior of the system to a greater extent than Berendsen, and hence is less
attractive when time-dependent features are of interest.

....hope this helps...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Mon Aug 16 2004 - 09:53:00 PDT
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