AMBER Archive (2003)

Subject: Re: AMBER: About Temperature Regulation

From: David A. Case (case_at_scripps.edu)
Date: Wed Dec 10 2003 - 10:30:24 CST

On Wed, Dec 10, 2003, L Jin wrote:
>
> I am a new user of AMBER. I am doing some testing or learning about AMBER. I
> have a problem about choosing the option for temperature regulation when
> running dynamics. If I use TAUTP=0.5, there will be a significant
> fluctuation of the energies, while TAUTP=5.0, the result will be better. I
> do not know how this option operate the temperature during dynamics.
> Therefore I do not know how to define it. Please give me some information
> about this. Thank you very much.
>

The weak coupling method of ntt=1 pretty much interpolates between the
canonical distribution (at small tautp) and NVE (constant energy Newtonian
dynamics) at large tautp. So there is no single best value, but most users
recommend against very small tautp values -- there are better ways to obtain
a canonical distribution.

See:

%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

..good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
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            |    http://www.scripps.edu/case
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