[gmx-users] FW: trjconv -dump problem

[Mark Abraham]

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
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