Sir, I am sorry I did not get any mail for that query since I posted it. So I had to ask once again..
1. g_energy -f ener.edr -o box.xvg selecting 15 16 17 0 2. gmxcheck -e ener.edr Opened ener.edr as single precision energy file frame: 0 (index 0), t: 0.000 Last energy frame read 50000 time 100000.000 Found 50001 frames with a timestep of 2 ps. 3. Gromacs version 4.5.3 This is the same data where I was mentioning that I was getting "not a number" (nan) error for all energy calculations under RMSD section. Thank you fro answering. With Regards M. Kavyashree On Fri, Jun 24, 2011 at 4:57 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Kavyashree M wrote: > >> Dear users, >> >> Any suggestions? >> >> > You haven't provided nearly enough diagnostic information for anyone to > offer you any useful help (as Mark said yesterday). For example, please > provide: > > 1. Your exact g_energy command line > 2. The output of gmxcheck for this .edr file > 3. Your Gromacs version > > -Justin > > Thank you >> M. Kavyashree >> >> >> On Thu, Jun 23, 2011 at 10:38 AM, Kavyashree M <hmkv...@gmail.com<mailto: >> hmkv...@gmail.com>> wrote: >> >> Dear users, >> >> In one of the simulations while calculating box dimensions >> using g_energy this output was obtained - >> Statistics over 50000001 steps [ 0.0000 through 100000.0000 ps ], 3 >> data sets >> All statistics are over 1978700 points >> >> Energy Average Err.Est. RMSD Tot-Drift >> ------------------------------**------------------------------** >> ------------------- >> Box-X 0.0453229 1.8 0.637535 -9.93022 >> (nm) >> Box-Y 0.0453229 1.8 0.637535 -9.93022 >> (nm) >> Box-Z 0.0320482 1.3 0.450805 -7.02173 >> (nm) >> >> but the dimensions of the box is different. plot attached. >> I am not able to figure out why only 1978700 data point are considered. >> Kindly give some suggestions. >> >> Thank you >> with regards >> M.Kavyashree >> >> >> > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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