[gmx-users] Fluctuations in NVT and NPT resulting plots
shima_arasteh2001 at yahoo.com
Sun Oct 21 12:32:57 CEST 2012
I got the plot for volume in the same way as I got plot for temperature in NVT. In this step, I just chose the volume instead of temperature after entering # g_energy -f nvt.edr.
I expected to see a flat line for this. Isn't it expectable?
Thanks for your kind reply.
----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, October 21, 2012 1:53 PM
Subject: Re: [gmx-users] Fluctuations in NVT and NPT resulting plots
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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