[gmx-users] trjconv -dump problem

[Peter C. Lai]

Dunno but try with -timestep 1?

Anyway, the .gro file emitted by mdrun contains the last frame anyway,
so there's not much reason to use trjconv to dump the last frame in the 
first place...

On 2012-02-13 04:19:45PM +0200, 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:
> 
>  
> 
> .
> 
> .
> 
> @ 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.
> 
>  
> 
> Thanks,
> 
> Ehud Schreiber.
> 
>  
> 

> -- 
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


-- 
==================================================================
Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|
==================================================================