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

[Shima Arasteh]

Thanks for your reply. Yes, I have done the complete tutorial of Lysozyme in water. I know the fluctuations seem usual but I don't know why they appears in the resulting plot.
In a NVT equilibrium, we are using an ensemble with a constant volume, so why the volume has sometimes big fluctuations ?




Sincerely,
Shima


________________________________
From: Arman Mahboubi Soufiani <armansoufiani at gmail.com>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, October 21, 2012 10:47 AM
Subject: Re: [gmx-users] Fluctuations in NVT and NPT resulting plots


Dear Shima,

I am not sure whether you have gone through Justin's tutorials or not. Moreover, how intense are your fluctuations?
You'd better take a look at the following link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html



On Sun, Oct 21, 2012 at 10:34 AM, Shima Arasteh <shima_arasteh2001 at yahoo.com> 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?
>
>Also I don't know the meaning of the fluctuations in pressure of NPT and temperature of NVT!
>
>Would you please give me an advice?
>
>
>Thanks in advance.
>Sincerely,
>Shima 
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