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 <[email protected] > 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 <[email protected]> > To: Shima Arasteh <[email protected]>; Discussion list for > GROMACS users <[email protected]> > 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 < > [email protected]> 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 > >-- > >gmx-users mailing list [email protected] > >http://lists.gromacs.org/mailman/listinfo/gmx-users > >* Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >* Please don't post (un)subscribe requests to the list. Use the > >www interface or send it to [email protected]. > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
