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Tsjerk On Wed, Aug 17, 2011 at 8:12 AM, Kavyashree M <hmkv...@gmail.com> wrote: > Dear users, > > While calculating the box dimensions during a simulation > of 20ns I got some strange values of the averages - > > Command used: > g_energy -f ener.edr -o box.xvg > > Output: > Energy Average Err.Est. RMSD Tot-Drift > ------------------------------------------------------------------------------- > Box-X 0.00665539 1.4 0.219101 -4.28575 (nm) > Box-Y 0.00665606 1.4 0.219101 -4.28574 (nm) > Box-Z 0.00470607 1 0.154928 -3.03048 (nm) > > While the actual dimensions are 7.2, 7.2 and 5.1 respectively. I use > Gromacs-4.5.3, and 4.5.4 version also gave the same error. But > when the .xvg file is examined it does not show much of the error > indicated here. I also checked whether the is any discontinuity in > the .edr file using gmxcheck and there was data from 0 to 20ns > with no such discontinuity. I am attaching the corresponding .xvg plot. > I had a similar problem before, and I was asked to check using > the new version. Which I did ad there was no difference. Meanwhile > I calculated the average values using other tools which gave 7.2, 7.2 > and 5.1 respectively. So What is the problem here. Kindly clarify the > confusion. > > Thanking you > With Regards > M. Kavyashree > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists