[gmx-users] Merging of two trajectories

[James Starlight]

Justin thanks,

Works perfect.


James

2012/7/18 Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>
> --
> ========================================
>
> 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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