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

[Justin A. Lemkul]

Miguel Quiliano Meza wrote:
> Dear Justin.
> 
> Thank you for you answer.
> 
> But, the case I wrote, it was an ideally case. To help anyone in the 
> forum at the same time.
> 
> As soon as I have read your answer I tried. In my case my simulations were:
> 
> First simulation: 0.4ns
> Second : 1ns
> Third: 2ns
> Fourth: 10ns
> ----------------------
> Total = 13.4ns
> 
> So I planned to do an RMSD plot of 0-13.4ns. As I said before, each 
> simulation is the continuation of the previous, obviously to do this I 
> used checkpoint files for each simulation and the same MD.mdp, only 
> changed the time of simulation.
> 
> I did:
> 
> trajcat -f md_0_4ns_noPBC.xtc md_1ns_noPBC.xtc md_2ns_noPBC.xtc 
> md_10ns_noPBC.xtc -o TOTAL_13_4ns_noPBC.xtc
> 
> Then for curiosity I did > ls -lh
> 
> rw-r--r-- 1 willy bioinfo   368M  2011-06-01 13:10 md_0_4_noPBC.xtc
> -rw-r--r-- 1 willy bioinfo  917M  2011-06-01 13:12 md_1ns_noPBC.xtc
> -rw-r--r-- 1 willy bioinfo  917M  2011-06-01 13:13 md_2ns_noPBC.xtc
> -rw-r--r-- 1 willy bioinfo  9.0G   2011-06-01 13:17 md_10ns_noPDB.xtc
> -rw-r--r-- 1 willy bioinfo  9.0G   2011-06-01 15:44 TOTAL_13_4ns_noPBC.xtc
> 
> Surprisingly the file "TOTAL_13_4ns_noPBC.xtc" had the same size of the 
> file "md_10ns_noPDB.xtc", is it normal?
> 

No, it's not.  But I don't know what you really typed.  For one, the command is 
not "trajcat," it's "trjcat."  As well, the file name is "md_10ns_noPDB.xtc," 
apparently, not "md_10_noPBC.xtc."  Please always copy and paste your commands 
from the terminal; due to the filename inconsistency I can't tell where the 
error is.  Please post:

1. The real command, copied and pasted
2. The output of gmxcheck on each of the .xtc files

Another problem is that you haven't used -settime (or maybe you did, but your 
command might not be transcribed properly), which would cause overlapping frames 
to over-write one another.

> Continue with the process, then:
> 
>  >g_rms -s molecule_sol_ion_MD_0_4ns.tpr -f TOTAL_13_4ns_noPDB.xtc -o 
> rmsd_13_4ns_molecule.xvg -tu ns
> 
> I open the .XVG as a simple .txt and I noticed that the time only reach 
> 10ns or 10000ps. Why not 13.4ns?
> 
> I would be very grateful If you can tell me what is happening.

I can't tell yet.  If you've omitted -settime, then you're overwriting frames 
and ending up with fragmented input.  If you're not specifying the correct 
filenames, you might be skipping times.

-Justin

-- 
========================================

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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