[gmx-users] Merging of two trajectories

[James Starlight]

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 ?

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

James



2012/7/18 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 7/18/12 7:35 AM, James Starlight wrote:
>>
>> Dear Gromacs Users!
>>
>>
>> I have two trajectories  with removed PBC which was done by the below
>> command.
>>
>> trjconv -s MD_B2ar_WP_3.tpr -f MD_B2ar_WP_3.trr -o md_noPBC.xtc -pbc
>> mol -ur compact
>>
>> Both of that trajectories are of the same system- when one trajectory
>> have been manyally stoped I've run the second one from the end of the
>> first trajectory using cpt file of the first simulation.
>>
>> I have no problem with that data but when I try to merge it by means
>> of VMD and obtain the whole file I noticed that new trajectory consist
>> of wrong kinetik data.
>>
>> E.g on the RMSD or some other graph the TIME values are always
>> incorrect. How I could prevent this and obtain correct whole
>> trajectory file from 2 or more parts?
>>
>>
>
> Use trjcat to concatenate the trajectories.  The -settime option will allow
> you to fix any potential issues with timestep, though if the simulations
> were all run with Gromacs and continued via .cpt file, there should be no
> need.
>
> -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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