[gmx-users] trjcat and trjconv

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> Hi 
> file1.xtc and file2.xtc are two consecutive MD trajectory files of the 
> same simulation system.
> 
> file1.xtc = 238 frames   (t=   0.00000   to t=   476.00000)
> 
> file2.xtc = 366 frames   (t=   0.00000   to t=   732.00000)
> 
> 
> 
> trjcat -f file1.xtc file2.xtc -cat -o file3.xtc
> 
> file3.xtc = 604 frames  =238+366
> 
> I did not get file3.xtc (t=   0.00000   to t=   1208.00000=476+732)
> 
> Instead, file3.xtc (t=   0.00000   to t=   476.00000  and then t=   
> 0.00000   to t=   732.00000)
> 

By using trjcat -cat, you are telling trjcat to not discard double time frames. 
  If both file1.xtc and file2.xtc start at t = 0, then trjcat detects that there 
are duplicated time frames, but instead just concatenates them anyway, since you 
are using -cat.

The better options are: (1) make sure that your starting times are what they 
should be, or (2) use trjcat -settime to manually specify the time at which each 
trajectory should start.

>  
> 
>  
> 
> trjconv -s file1.tpr -f file3.xtc -o file4.xtc -dt 100
> 

As advised in the trjconv help information, it is much easier to concatenate 
trajectories using trjcat, but essentially this is manifesting the same behavior 
described above.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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