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
