[gmx-users] [Fwd: trjcat]

[David]

-------- 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.

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

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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