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

[Andrew DeYoung]

Hi Justin,

Thanks so much for your time.  

You make a very good point about NPT.  My field (although I am only a
second-year graduate student) is physical chemistry, and I am ignorant,
unfortunately, of biochemical literature.  

In physical chemistry, it seems that people almost always use NVT for
production simulations, but I am not sure why, because just as in
biochemical lab experiments, I would expect NPT to be more realistic --
chemicals (whether it is a pure liquid, like in "my" field, or a solvated
biomolecule, like in "your" field) are usually exposed to atmospheric
pressure in experiments.  In experiments, the volume is usually not fixed, I
think.  So it makes sense you say that biochemical simulations are typically
performed in NPT.  I don't know why physical chemistry experiments on, and
simulations of, liquids would be any different.

I guess then this could be an issue of the field?  Are there chemists or
physicists reading this that can please provide advice?

Best wishes,

Andrew DeYoung
Carnegie Mellon University