[gmx-users] Merging of two trajectories

[Justin Lemkul]

On 7/18/12 9:34 AM, James Starlight wrote:
> Justin
>
> thanks for advise
>
> I've used the bellow command for both trajectory
>
> trjcat -f md_noPBC.xtc md_noPBC_GO.xtc -tu ps -o merged_noPBC.xtc
>
> but resulted  merged_noPBC.xtc consist of data from only second
> trajectory although in the log file both trajectories have been
> processed
>
>            File             Current start (ps)  New start (ps)
> ---------------------------------------------------------
>               md_noPBC.xtc        0.000 ps          0
>            md_noPBC_GO.xtc        0.000 ps          0
>
> Summary of files and start times used:
>
>            File                Start time       Time step
> ---------------------------------------------------------
>               md_noPBC.xtc        0.000 ps        7.000 ps
>            md_noPBC_GO.xtc        0.000 ps        7.000 ps WARNING:
> same Start time as previous
>
>
> Back Off! I just backed up merged_noPBC.xtc to ./#merged_noPBC.xtc.5#
> Reading frame       0 time    0.000
> Reading frame    3000 time 21000.000
> Reading frame       0 time    0.000
>
> Continue writing frames from md_noPBC_GO.xtc t=0 ps, frame=0
> Reading frame   10000 time 70000.000    ->  frame  10000 time 70000.000 ps
>
> Last frame written was 10008, time 70056.000000 ps
>
> Why this occurs ?

Because you're telling trjcat that both trajectories start at the same time, so 
they're going to overwrite one another.  If they are indeed two separate 
segments of a continuous trajectory, they need different start times, one zero 
and one non-zero.

>
> By the way if I'm using -cat option resulted file consist of both
> trajectories ( in the separate enties).

That's what -cat is designed to do.  I doubt you want that in this case.  The 
times will still be wrong.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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