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

[Kukol, Andreas]

Use trajcat with the option -settime then you can specify the starting time for each simulation interactively.

Andreas
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Miguel Quiliano Meza [rifaximina at gmail.com]
Sent: 01 June 2011 20:34
To: gmx-users at 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.