[gmx-users] trjconv -dump problem

Ehud Schreiber schreib at compugen.co.il
Mon Feb 13 15:19:45 CET 2012

Dear Gromacs users,


I minimized a protein structure 1IARcompleted_WT.pdb, getting, among
others, the files 1IARcompleted_WT_minimized.trr and
1IARcompleted_WT_minimized_potential_energy.xvg . Looking at the latter
file showed the last frame to be at 217 ps:




@ s0 legend "Potential"

    0.000000  -31997.519531

    0.000000  -33810.406250

  200.000000  -69850.609375

  217.000000  -69898.031250


I wanted to extract only this last frame from the .trr file, so used


trjconv  -f 1IARcompleted_WT_minimized.trr -o
1IARcompleted_WT_minimized_217.trr -dump 217


However, this seems to have produced a file with the t = 200 ps
conformation, though the dump parameter was recorded, as trjconv output




Option       Type   Value   Description




-dump        time   217     Dump frame nearest specified time (ps)



Will write trr: Trajectory in portable xdr format

trn version: GMX_trn_file (single precision)

Reading frame       2 time  200.000   

Dumping frame at t= 200 ps

Reading frame       3 time  217.000   




Also, using -dump 200 gave an identical file to the above.


Any idea why the expected timeframe isn't reproduced?

I'm using gromacs 4.5.3.



Ehud Schreiber.


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