[gmx-users] RE: trjconv -dump problem

[Ehud Schreiber]

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 <Mark.Abraham at anu.edu.au>>
> Subject: Re: [gmx-users] FW: trjconv -dump problem
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>>
> Message-ID: <4F3A3E42.6000605 at anu.edu.au>>
> 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