Sir, I checked gmxdump -e ener.edr as suggested, I found that there are exactly 10001 values for Box-X/Y/Z with 7.,7 and 5 when I calculated the average for these values using another tool I got 7.2, 7.2 and 5.1 as expected. But g_energy gave some different answer as mentioned before in both 4.5.3 and 4.5.4 versions. Sorry I sent the mail twice as I did not receive Dr. Mark's reply form the forum.
Thank you With Regards Kavya On Wed, Aug 17, 2011 at 4:15 PM, Kavyashree M <hmkv...@gmail.com> wrote: > Sorry Sir, > > I did not get that mail from the forum. > > Thank you > With Regards > Kavya > > > On Wed, Aug 17, 2011 at 12:11 PM, Tsjerk Wassenaar <tsje...@gmail.com>wrote: > >> This mail was answered already... Please pay attention. >> >> http://lists.gromacs.org/pipermail/gmx-users/2011-August/063814.html >> >> 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 >> > >
-- 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