Re: [AMBER] barostat with large coupling constant

From: Jason Swails <>
Date: Wed, 4 Oct 2017 15:58:20 -0400

On Wed, Oct 4, 2017 at 12:16 PM, R zu <> wrote:

> I am sorry about the point of Berendsen barostat.
> One comparison of the barostats says it doesn't give the correct average.

​It gives the correct average pressure, but the wrong average isothermal
compressibility (which is a function of the size of the fluctuations, which
are incorrect with the Berendsen barostat).

> The reference 5 and 6 link to the the flying ice cube problem, and
> collective motion artifacts.

​Flying ice cube can be corrected by removing center-of-mass motion
periodically, which is done by default within Amber.

> I guess the problem is that it would take forever to get the correct
> ​​
> average?

​Assuming you mean correct average compressibility, then no. The problem
is not that it would take forever to get the correct average -- the problem
is that it doesn't sample from the isobaric-isothermal ensemble. So the
limiting distribution has an incorrect thermodynamic average for the
compressibility. So even if you wait forever, the average compressibility
will still be wrong.


Jason M. Swails
AMBER mailing list
Received on Wed Oct 04 2017 - 13:00:03 PDT
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