Re: [AMBER] DIfferences between thermostats

From: David A Case <>
Date: Tue, 22 Nov 2016 20:36:46 -0500

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.


AMBER mailing list
Received on Tue Nov 22 2016 - 18:00:02 PST
Custom Search