[gmx-users] Conceptual question: Why are MD production simulations usually run in the NVT ensemble?

[Andrew DeYoung]

Hi,

I'm not sure if this is an appropriate question for the Gromacs users'
mailing list.  If it isn't, please forgive me and disregard this message.

I asked this question on Physics Stack Exchange: Why is the canonical (NVT)
ensemble often used for molecular dynamics (MD) simulations?  My question
and an answer are posted here:

http://physics.stackexchange.com/questions/31997/why-is-the-canonical-nvt-en
semble-often-used-for-classical-molecular-dynam

My question is, do you agree with the answer?  I'm not sure that I do.  The
responder seems to imply that it is practically impossible to use periodic
boundary conditions in an NPT simulation.  But, I think that the algorithms
in Gromacs do just this; am I correct in this belief?

People do often run _equilibration_ simulations in the NPT ensemble, I
think.  They do this usually, I think, to obtain the proper density -- the
code changes the box dimensions until the proper average pressure is
reached.  Then, for _production_ simulations, people usually use the NVT
ensemble, where the dimensions of the simulation box are held fixed.  My
question here is, why is the NVT ensemble, rather than the NPT ensemble,
typically used for production MD simulations?

Do you have any suggestions for helpful reading that I can do on this topic?
Thank you for your time! 

Andrew DeYoung
Carnegie Mellon University