On 16/08/11, 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. Kindly clarify the confusion. >
That looks like a bug in g_energy. What does gmxdump -e ener.edr have to say about the BoX-?? values? Mark
-- 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
