Re: [AMBER-Developers] default for gamma_ln?

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 10 Mar 2015 19:54:57 -0400

On Tue, Mar 10, 2015 at 6:54 PM, Alexey Onufriev <alexey.vt.edu> wrote:

> Hi, All.
>
> I am wondering what was the original logic for setting the default value of
> zero
> for gamma_ln (Langevin thermostat)? It duplicates ntt=0, which seems a more
> logical choice if one wants constant energy. For gamma_ln default we can
> use e.g. 0.01 ps^-1, which we would recommend in practice. Thoughts?
>

‚ÄčI have no strong feelings either way. I always think of Langevin not as a
thermostat, but rather as an integrator for a different set of equations of
motion (one with a stochastic element).

It just so happens that when the collision frequency is 0, those EOMs
become identical to standard Newton's equations. Perhaps that was the
rationale? (Much like the default behavior for the standard integrator is
to *not* have temperature control)

All the best,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 10 2015 - 17:00:02 PDT
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