Hello Justin, I am using Gromacs 4.0.7 Actually, I am joining around 20 trajectories of around 300 ns each. Its a CGMD run. But I reported here only those two trajectories between which trjcat has shown the warning while joining. So what should i do?
Thanks, Anirban On Thu, May 5, 2011 at 7:58 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Anirban Ghosh wrote: > >> Hello Justin, >> >> Thanks for the reply. >> gmxcheck on the first trajectory shows: >> >> >> ------------------------------------------------------------------------------------------------- >> Checking file protein_3000NS_2.trr >> trn version: GMX_trn_file (single precision) >> Reading frame 0 time 2957280.000 # Atoms 57296 >> Reading frame 1400 time 2999280.000 >> Item #frames Timestep (ps) >> Step 1425 30 >> Time 1425 30 >> Lambda 1425 30 >> Coords 1425 30 >> Velocities 1425 30 >> Forces 0 >> Box 1425 30 >> >> --------------------------------------------------------------------------------------------------- >> >> And on the second trajectory shows: >> >> >> --------------------------------------------------------------------------------------------------- >> Checking file B2AR_self_assembly_3500NS.trr >> trn version: GMX_trn_file (single precision) >> Reading frame 0 time 3000000.000 # Atoms 57296 >> Reading frame 16000 time 3480000.000 >> Item #frames Timestep (ps) >> Step 16667 30 >> Time 16667 30 >> Lambda 16667 30 >> Coords 16667 30 >> Velocities 16667 30 >> Forces 0 >> Box 16667 30 >> >> --------------------------------------------------------------------------------------------------- >> >> So gmxcheck does not show any warning/error. >> Then why I am getting the warning from trjcat. And how to remove it? >> >> > I don't know yet. A few more questions: > > 1. What version of Gromacs are you using? > > 2. How many total trajectories are you concatenating? You said there was a > problem from 10 -> 3000000 ns, but I don't see any times shown here below > 2957280. The real problem could be early on in the trajectory. > > -Justin > > Thanks, >> >> Anirban >> >> >> On Thu, May 5, 2011 at 7:19 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Anirban Ghosh wrote: >> >> >> Hi ALL, >> >> I am trying to use trjcat -f input files -o output_file to join >> to very larger trajectories. However I am getting the following >> error: >> >> >> >> ------------------------------------------------------------------------------------------------------------------------------------------- >> Continue writing frames from protein_3000NS_2.trr t=2.95728e+06 >> ps, frame=98576 -> frame 100000 time 3000000.000 ps -> >> frame 99980 time 2999400.000 ps WARNING: Frames around >> t=3000000.000000 ps have a different spacing than the rest, >> might be a gap or overlap that couldn't be corrected automatically. >> Reading frame 0 time 3999990.000 lasttime 3e+06 >> >> Continue writing frames from protein_4000NS.trr t=3.99999e+06 >> ps, frame=100001 >> >> ------------------------------------------------------------------------------------------------------------------------------------------- >> >> And if I use this resultant output trajectory for further >> analysis like g_sas, then a portion between around 10 ns and >> 3000000 ns is simply joined by a straight line. >> How to remove this inconsistency from the two trajectories? >> Any suggestion is welcome. >> >> >> What does gmxcheck tell you about each of the individual >> trajectories (prior to running trjcat)? >> >> -Justin >> >> -- ======================================== >> >> 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 >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> 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 gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read 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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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