[gmx-users] [Fwd: trjcat]

[David]

On Tue, 2005-11-22 at 21:33 +0100, David wrote:
> -------- Forwarded Message --------
> From: Una Bjarnadottir <una.bjarnadottir at ucd.ie>
> To: spoel at xray.bmc.uu.se
> Subject: trjcat
> Date: Tue, 22 Nov 2005 18:52:39 +0000
> Dear David,
> 
> I sent a trouble to the mailing list but didn't receive any help on it.
>   I hope you don't mind me sending it to you personaly because so far I
> have not find out how to use trjcat properly.
I do mind because it gives me double work.

> 
> Here is my letter to the mailing lis;
> 
> Hi everybody,
> 
> I'm trying to make one .trr file from runs I had to restart.  Like I
> understood it you put your crashed runs in order;
> 
> trjcat -f md1.trr md2.trr -o md_appended.trr
> 
first run gmxcheck on both trajectories. Probably one is missing a lot
of frames. Otherwise run gmxcheck on the resulting trr. You may also
have a 2 Gb problem.

> Than I got;
> Reading frame       0 time  279.000
> Summary of files and start times used:
>             File                Start time
> -----------------------------------------
>            md1.trr               0.000 ps
>            md2.trr             279.000 ps
> Reading frame       0 time    0.000
> lasttime -12345
> Continue writing frames from md1.trr t=0 ps, frame=0
> Last frame       2800 time  280.000    ->  frame   2780 time  278.000 ps
> Reading frame       0 time  279.000
> lasttime 278.9
> Continue writing frames from md2.trr t=279 ps, frame=2790
> Last frame      47210 time 5000.000    ->  frame  50000 time 5000.000 ps
> Last frame written was 50000, time 5000.000000 ps
> 
> And my run was total 5000ps.  But when using trjconv I only got 299
> snapshots but not 500 as I expected!
> 
> trjconv -f md_appended.trr -s .gro/.tpr -o .pdb -n 1ATP_SEP_140905.ndx
> -sep -skip 100
> 
> Select a group: 3
> Selected 3: 'C-alpha'
> trn version: GMX_trn_file (single precision)
> Last frame      29900 time 2990.000    ->  frame    290 time 2900.000
> WARNING: Incomplete frame: nr 29901 time 2990.1
> 
> Didn't I use trjcat right and how is it supposed to be used?  The only
> thing I found regarding this matter on the web said I had to use trjconv
> -b -e before trjcat but I don't understand why that had to be done if
> trjcat takes the time in the beginning anyway.
> 
> Please help and best regards to you:)
> 
> Also I found trjcat –o trajout traj1 traj2, where traj1 and traj2 must
> be the files that has to been put togather but when trying to use that I
> get that traj1 and traj2 are unknown arguments!
> 
> Can you plesae help me,
> 
> With my very best, Una Bjarnadottir
> 
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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