Sir, I went through the whole .edr file for one specific term in which I was getting nan. Of the three columns (Energy; Av. Energy; Sum Energy) order (power) for temperature did not change at all in the first column but in the second column there was a change of power between +1 and +2 which was +2 in another .edr file from other simulation. ven though the second column value is arround 1--e+02 while those with +1 power is around 9.--e+01 which is quite near to 1.--e+02.
But I did not find any huge changes in the temperature. Thank you With Regards M. Kavyashree On Fri, Jun 24, 2011 at 5:53 PM, Kavyashree M <[email protected]> wrote: > Sir, > > I tried it already but It was huge file. this kind of nan comes only > for RMSD not for any other term. I will try looking into that file again. > > Thanks > With regards > M. Kavyashree > > > > > On Fri, Jun 24, 2011 at 5:20 PM, Justin A. Lemkul <[email protected]> wrote: > >> >> >> Kavyashree M wrote: >> >>> 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. >>> >>> >> I've said several times before that this energy file is probably junk, and >> again I'd suspect that. The only thing to check would be to run gmxdump on >> the .edr file (and redirect into some output file or pipe the output through >> "more" to actually see it) and see where the energy values go screwy. If >> you find a bunch of nonsensical information, then you have your answer. >> >> -Justin >> >> Thank you fro answering. >>> >>> With Regards >>> M. Kavyashree >>> >>> >>> On Fri, Jun 24, 2011 at 4:57 PM, Justin A. Lemkul <[email protected]<mailto: >>> [email protected]>> 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 >>> <[email protected] <mailto:[email protected]> >>> <mailto:[email protected] <mailto:[email protected]>>> 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 <http://vt.edu> | (540) 231-9080 >>> >>> >>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >>> >>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> > >>> >>> ==============================**__========== >>> -- gmx-users mailing list [email protected] >>> <mailto:[email protected]> >>> >>> >>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >>> >>> <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> >>> >>> <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 [email protected] >>> <mailto:gmx-users-request@**gromacs.org<[email protected]> >>> >. >>> >>> Can't post? Read >>> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >>> >>> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> >>> >> -- >> ==============================**========== >> >> 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 [email protected] >> 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 [email protected]. >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >
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