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 <[email protected]> To: Shima Arasteh <[email protected]>; Discussion list for GROMACS users <[email protected]> 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 ======================================== -- 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
