On Wed, Dec 02, 2015, jfliu wrote:
>
> Can anyone tell me how the gamma_ln value affects the temperature
> in Langevin dynamics during the MD simulation ?
> From the Amber manual, I see it is usually set to 2.0 ~ 5.0 /ps. I want
> to know, what value can I use to obtain a more stable temperature during
> the MD simulation ? i.e., the larger gamma_ln, the more stable
> temperature ？ or, the inverse ?
I think the discussion of choice of gamma_ln goes back a long way, but one of
the original papers is still very relevant:
%A R.J. Loncharich
%A B.R. Brooks
%A R.W. Pastor
%T Langevin dynamics of peptides: The frictional dependence of isomerization
rates of N-actylananyl-N'-methylamide
%J Biopolymers
%V 32
%P 523-535
%D 1992
The choice of friction constant should not affect the average temperature or
other equilibrium properties, but will affect the time scales of motion.
Small values like 2-5 ps^-1 are an attractive compromise, generally giving
good temperature regulation without supressing dynamical transition.
If you are not getting "stable temperature" (not sure what that means) with a
gamma_ln of 5.0, there is a good possibility that something else is wrong with
the simulation or the force field you are using. [It's possible that you just
have an unusual system: most empirical experience is on proteins and nucleic
acids.]
....dac
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Received on Wed Dec 02 2015 - 06:30:04 PST
