AMBER Archive (2003)

Subject: Re: AMBER: About Temperature Regulation

From: L Jin (s0344557_at_sms.ed.ac.uk)
Date: Wed Dec 10 2003 - 11:06:25 CST

Thank you very much for answering. Yes, I agree with choosing small TAUTP as
mentioned in the Manual. But there seems to be a conflict.

Manual: smaller value ----- tighter coupling to the heat bath----- smaller
fluctuations in kinetic energy, but larger fluctuations in the total energy;

My result: When TAUTP=0.5, all of the energies (including the kinetic energy)
jump up-and-dow significantly up to 200Kcal/mol, while TAUTP=5.0 they keep in a
relative good scale of about 20Kcal/mol. My molecule is a monosaccharide, so I
think there should not be such a large scale of energy changing.

Lan

Quoting "David A. Case" <case_at_scripps.edu>:

> 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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