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.
http://www.gromacs.org/Documentation/Terminology/Pressure
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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