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

[Shima Arasteh]

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.


 
Sincerely,
Shima


----- 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>
Cc: 
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.

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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