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

[Arman Mahboubi Soufiani]

I am sorry that I cannot help you more with this case. I am kind a
beginner. Hopefully, you will receive useful responses soon.

BR

Arman

On Sun, Oct 21, 2012 at 10:57 AM, Shima Arasteh <shima_arasteh2001 at yahoo.com
> wrote:

>
>
> 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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