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 <[email protected]>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 <[email protected]> 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 [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 > > > > > > -- > 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 [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 >
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