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

From: Jason Swails <>
Date: Fri, 5 Jul 2013 21:23:58 -0400

On Fri, Jul 5, 2013 at 9:16 AM, Yip Yew Mun <> wrote:

> Thanks David.! At least I now understand why I'm running NPT most of the
> time. But is there any significance in running NVT for a certain time
> frame, then continue with NPT, for MD simulations.? (I'm picking
> statistical mechanics currently. :)

In addition to what Dave said, there's the added complexity of 'what do I
choose from a computational perspective, and why?' I actually rarely run
NPT simulations since they tend to be noticeably more expensive than NVT
simulations, and for systems that are nowhere near a phase transition the
various ensembles tend to be indistinguishable. But it also depends on
what you want to learn. If you want to measure time-dependent properties,
like diffusion for instance, you need to use NVE with good settings for
energy conservation.

My suggestion is to look at the protocol followed by projects you encounter
in your literature search. Certain texts are also quite helpful (I'll give
another plug for the Allen and Tildesley text, which I've found to be quite
insightful). The Tuckerman Statistical Mechanics book is also a pretty
good choice IMO.

I'll also echo that a true treatise on this subject is well beyond the
scope of an email chain on a mailing list (and is beyond the scope of most
single textbooks as well).

Good luck,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Fri Jul 05 2013 - 18:30:02 PDT
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