Re: [AMBER] DIfferences between thermostats

From: Markowska <>
Date: Wed, 23 Nov 2016 09:14:47 +0100

Thank you very much for your help.

We have tested the Berendsen thermostat, but in MD of a similar system we
observed the "flying ice cube" effect. So we've change the thermostat to
Langevin with gamma_ln value of 1.0. I'll check the smaller value.

And what about the hydrophobic properties of amino acids? Does the
thermostat affect these properties?

I really appreciate your help :)
Have a nice day!

W dniu środa, 23 listopada 2016 David A Case <>

> On Tue, Nov 22, 2016, Dave Cerutti wrote:
> > Yes, fair enough--Berendsen is bad, I'm with Bernie (Brooks)! A very
> weak
> > Berendsen thermostat is what was recommended to me for simulations where
> > diffusion properties and NVT are needed simultaneously, by one of our
> > respected colleagues no less. And, I agree--formally, it's bad, but with
> > weak thermocoupling, in practice the effects are negligible.
> In the bad old days, we used Berdensen and got "flying blocks of ice". We
> found that by tightening up tolerances one could more or less get rid of
> this. But that was for runs of dozens of nanoseconds. I recently thought
> I could use a weak Berdensen thermostat just to keep the overall energy
> from drifting. Seemed to work great for about 8 microseconds, at which
> point the protein froze--just like the old days, but now after 100 times
> longer simulation. Rules of thumb that seemed good for simulations of
> 10^7 steps may fail for runs of 10^10 steps.
> I suspect (following work from Leimkuhler, Izaguirre, Skeel, etc.) that
> Langevin with a really good random number generator and a very low
> collision
> constant would have been a better choice for me. But I don't have personal
> experience to back that up.
> ...dac
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Received on Wed Nov 23 2016 - 00:30:03 PST
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