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

[Miguel Quiliano Meza]

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.

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?

Thank you in advance.

Miguel Quiliano.
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