Sir, Thats right. But what I felt was, all these problems are connected. (I dont mean that temperature is connected to box dimension) Actually I was getting nan under RMSD for all the energy terms.
I have checked the total energy graph also it is stable. even in case of box dimentions I checked the box dimensions for the whole trajectory for eg. Box-X most of the time has value around 9. very few times it gets a value near 8.9.. Thank you With Regards M. Kavyashree On Fri, Jun 24, 2011 at 6:18 PM, Justin A. Lemkul <[email protected]> wrote: > > > Kavyashree M 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. >> >> > Let's keep on topic and focus on the box vectors; changing the subject > midway makes it harder to arrive at a solution. The only diagnostic I can > suggest is gmxdump. It should be rather obvious what's going on - your > reported averages are 0.04, but the actual values from the plot are clearly > different. > > -Justin > > Thanks >> With regards >> M. Kavyashree >> >> >> >> On Fri, Jun 24, 2011 at 5:20 PM, Justin A. Lemkul <[email protected]<mailto: >> [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]> >> <mailto:[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]>> >> <mailto:[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> <http://vt.edu> | (540) >> >> 231-9080 >> >> http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin >> >> <http://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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> >> >> >> ==============================**____========== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[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> >> > >> >> <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> >> > >> >> <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]> >> > >> <mailto:gmx-users-request@__gr**omacs.org <http://gromacs.org> >> <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> >> > >> >> <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 <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. 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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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