Use trajcat with the option -settime then you can specify the starting time for
each simulation interactively.
Andreas
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Miguel Quiliano Meza [rifaxim...@gmail.com]
Sent: 01 June 2011 20:34
To: gmx-users@gromacs.org
Subject: [gmx-users] question about trajcat command: Merge files
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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