[gmx-users] Re: Conceptual question: Why are MD production simulations usually run in the NVT ensemble?
adeyoung at andrew.cmu.edu
Sat Jul 14 18:55:42 CEST 2012
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?
Carnegie Mellon University
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