On Mon, Oct 26, 2015 at 8:34 AM, Karolina Markowska <markowska.kar.gmail.com
> wrote:
> Hello!
>
> I looks like everything is OK now with my simulations. Once again thank you
> for your help.
> Could someone explain me something more about that "flying block of ice
> effect"?
>
https://en.wikipedia.org/wiki/Flying_ice_cube
And one of the primary citations (listed at the bottom of the Wikipedia
page):
http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-987X(199805)19:7%3C726::AID-JCC4%3E3.0.CO;2-S/abstract;jsessionid=1FCE9513DB953FC54DDC23E44CB1BC08.f03t03
> And I would appreciate if you also tell me some differences between the
> Berendsen and Langevin thermostat. Maybe there is a paper about these two
> thermostats?
>
Berendsen is a very simplistic approach in which a target temperature is
reached by simply scaling the velocities either up or down to reach the
target temperature. Langevin is a different type of integrator that uses a
stochastic (random) component to emulate solvent collisions (or friction).
Berendsen does *not* produce a valid canonical ensemble while Langevin
integration does.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Oct 26 2015 - 06:00:08 PDT
