[gmx-users] question about trajcat command: Merge files

[Justin A. Lemkul]

Miguel Quiliano Meza wrote:
> Dear community,
> 
> I have a couple of doubts, please help me to clarify.
> 
> I performed 4 MD simulations using Gromacs (each one of 1ns, 2ns, 3ns 
> ,4ns) , they are only a continuation of the last, because of I was 
> explored the rmsd variation along the time. Now I want to merge all the 
> trajectories to do only one plot of 10ns.
> 
> So, I did:
> 
> trajcat -f md_1ns_noPBC.xtc md_2ns_noPBC.xtc md_3ns_noPBC.xtc 
> md_4ns_noPBC.xtc -o TOTAL_10ns_noPBC.xtc
> 
> The program showed this:
> 
> File                Start time       Time step
> ---------------------------------------------------------
>          md_1ns_noPBC.xtc        0.000 ps        2.000 ps
>          md_2ns_noPBC.xtc        0.000 ps        2.000 ps WARNING: same 
> Start time as previous
>          md_3ns_noPBC.xtc        0.000 ps        2.000 ps WARNING: same 
> Start time as previous
>          md_4ns_noPDB.xtc        0.000 ps        2.000 ps WARNING: same 
> Start time as previous
> 
> I am worry about the message 'WARNING: same Start time as previous', I 
> think is normal because each simulation is like independent, that is the 
> reason why start time is take as 0ps.
> 

This may be correct for your case (if in the .mdp file you have "tinit = 0") or 
you otherwise did not properly continue the simulation using a checkpoint file. 
  If it makes sense to concatenate independent trajectories and consider them to 
be continuous, you can override the start times with the -settime option.

> Please tell me If my command line is correct according to my purposes. 
> By the way, to make the plot (RMSD 10ns) I plan to do it with -s 
> md_1ns.tpr, is it correct?
> 

That will calculate RMSD relative to the structure contained in the .tpr file 
that began the first 1-ns simulation.  If that's what you wish to measure, then 
you're correct.

-Justin

-- 
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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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