[gmx-users] Fluctuations in NVT and NPT resulting plots

Justin Lemkul jalemkul at vt.edu
Sun Oct 21 12:23:05 CEST 2012

On 10/21/12 3:04 AM, Shima Arasteh wrote:
> Dear gmx users,
> As I know, NVT equilibration is done on a ensemble with a constant V . I got the volume plot versus time. The resulting plot has some fluctuations. I don't know what it means?! Does it make sense?

I don't understand how you got a plot of volume vs. time for NVT.  Volume and 
box vector terms are not stored in an NVT .edr file; they are fixed quantities.

> Also I don't know the meaning of the fluctuations in pressure of NPT and temperature of NVT!

"Constant" does not mean "fixed."  The values will oscillate about the desired 
quantity and will stabilize when equilibration is finished.  Pressure 
fluctuations in NPT will always be fairly large.




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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