Langevin is a better thermostat than Berendsen for most applications, but
at most useful strengths it will interfere with dynamical calculations such
as diffusion or residence times. (Because, what's physical about having
particles of an ethereal bath collide with every atom at every step of the
simulation?) The Andersen thermostat is also going to interfere with
diffusion calculations. In either case, you must make sure that you are
not restarting the simulation with the same random seed, as repeating
sequences of random numbers will drive artifacts. These include unfolded
proteins in the strong case (restarts every 10,000 steps), slight
instability in the more sinister weak case (restarts every 100,000 steps),
with the effects becoming negligible below a Langevin gamma_ln of 3.0 and
restarts every 1,000,000 steps.
The only thermostat that wouldn't seriously affect diffusion would be a
weak Berendsen thermostat, but for dynamics you'd probably want to just go
to NVE anyway. Note, however, that I'm not using dynamics and structural
degeneracy interchangeably. If your protein has a floppy loop then
simulations with any thermostat, Langevin included, will explore its
conformations just fine.
Dave
On Tue, Jun 25, 2019 at 2:20 PM James Starlight <jmsstarlight.gmail.com>
wrote:
> Dear Amber Users!
>
> At present moment, I am dealing with the modeling of the enzymes from
> xylanase subfamily, which have several flexible loops of crusial
> functional importance in shielding of the active site and thus in
> being significative for tayloring of the enzyme to its substrate.
>
> Could you tell me which thermostat that had been emplemented in Amber
> should be better option to reproduse dynamics of such inherently
> dynamical systems (with flexible loops) assuming that I model it with
> complex with substrate (sugar, parametrized by GLYCAM) as well as in
> the apo-state?
>
> Notably, actually I have tried to use Berendsen method, which probably
> was not good solution for the modeling in nanosecond range.
>
> # equilibrate
> ntt=1, tempi=0.5, temp0=310.0,
> #run production
> ntt=1, tempi=0.1, temp0=310.0,
>
> May the switching to Langeving dynamics in the following manner be
> better for the modeling of such system?
>
> #run equilibration
> ntt=3, temp0=310, gamma_ln=5
> #run production
> ntt=3, temp0=310, gamma_ln=1
>
> Yours with thanks,
>
> Prof. James Starlight Jr.
>
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>
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Received on Tue Jun 25 2019 - 12:00:02 PDT
