Re: [AMBER] A General Question with regards to the NVT & NPT ensembles in MD Simulations

From: David A Case <>
Date: Fri, 5 Jul 2013 09:01:28 -0400

On Fri, Jul 05, 2013, Yip Yew Mun wrote:
> It's kind of a newbie question, but I wish to ask what's the difference
> between using the NVT & NPT ensembles in MD simulations, especially in
> the case of proteins? Because I seem to be running simulations under
> the NPT ensembles and I don't seem to know why. So I wish to know what
> quantities am I trying to measure when I use different ensembles in MD
> simulations?

The problem is not that this is a "newbie" question, but rather that the
answer is rather too general and complex for a mailing list discussion.

For large enough systems (and a protein in water is generally "large enough")
there is little difference between ensembles. But, as a practical matter, you
need to use NPT simulations during equilibration of liquid systems to get the
correct density (since the initial density won't be correct in general). Once
equilibration is over, most properties of proteins are pretty insensitive to
a change between NVT and NPT (or even NVE).

A next good step would be to look at a textbook on statistical mechanics, or
the classic text on liquid simulations by Allen & Tildesley.

[Longer winded, somewhat more advanced:]

(a) Arguably, NPT is closest to the physical setup of most experiments,
but time-dependent behavior is then suspect.

(b) The Berendsen barostat used in Amber does not given the canonical
behavior, suppressing volume fluctuations, especially if taup is much
greater than 1ps. (We will have better barostats in the next release).

(c) The only sure way I know to get correct results is to run NVE
simulations in systems large enough to approach the thermodynamic limit.
This is rarely done.

(d) The "correct results" referred to in part (c) assume classical
mechanics; nuclear quantum effects being ignored are likely to be as or
more important than are differences between ensembles.

(e) errors in force fields probably swamp all the concerns of the
paragraphs above.

...good luck...dac

AMBER mailing list
Received on Fri Jul 05 2013 - 06:30:02 PDT
Custom Search