Dear Mark (or anybody else interested), The .trr file does include the final (t = 217) frame - first, trjconv said: Reading frame 3 time 217.000 and second this is verified by converting the whole trajectory to .gro: trjconv -f 1IARcompleted_WT_minimized.trr -s 1IARcompleted_WT_minimized.tpr -o 1IARcompleted_WT_minimized_path.gro
It therefore seems the behavior is a bug, as the last frame is there, and is needed, especially in minimizations. An output in a .gro format is not sufficient for a further minimization because of its limited accuracy format of coordinates. Also, my mdrun did not produce a checkpoint file (I'm not sure whether because I didn't ask to or because the run was shorter than 15 minutes). Thanks, Ehud Schreiber. > ------------------------------ > > Message: 2 > Date: Tue, 14 Feb 2012 21:58:10 +1100 > From: Mark Abraham <[email protected]>> > Subject: Re: [gmx-users] FW: trjconv -dump problem > To: Discussion list for GROMACS users <[email protected]>> > Message-ID: <[email protected]>> > Content-Type: text/plain; charset="iso-8859-1" > > On 14/02/2012 7:59 PM, Ehud Schreiber wrote: >> >> 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: >> >> . >> . >> >> @ title "Gromacs Energies" >> @ xaxis label "Time (ps)" >> @ yaxis label "(kJ/mol)" >> . >> . >> @ 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 was: >> >> . >> . >> 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. >> > > Your nstxout parameter means not every frame is written. > Prior to the implementation of checkpointing, the final frame was written to the .trr regardless of nstxout, but that no longer occurs. > The final frame is in your checkpoint file, and you can use that anywhere you might use a coordinate file - including trjconv to get a simple coordinate file from it. > > Mark -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
