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? Thanks, Anirban On Thu, May 5, 2011 at 7:19 PM, Justin A. Lemkul <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 | (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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