[gmx-users] trjcat -cat skips frames

[Michel Cuendet]

Hi all,

I have 162 small independent trajectories (from time 100 to time 300ps, 
2ps interval) in directories named 1/ ... 162/. I want to merge them 
into one big trajectory for analysis purposes:

trjcat -cat -o traj_tot.xtc -f */traj.xtc

trjcat seems to start skipping some frames after about the 100th 
trajectory. It does not start reading at time 100 anymore. Total number 
of frames is 15432 instead of the 162*101 = 16632 that it should be. 
Output looks like below.

Concatenating the trajectories in two batches of about 80 trajectories 
each and then combining the two resulting files together works.

Cheers,
Michel

===================================================================

Reading frame       0 time  100.000   

Continue writing frames from 100/traj.xtc t=100 ps, frame=0      
Last frame        100 time  300.000    ->  frame    100 time  300.000 ps     
Reading frame       0 time  100.000   
lasttime 300

Continue writing frames from 101/traj.xtc t=100 ps, frame=101      
Last frame        100 time  300.000    ->  frame    200 time  298.000 ps     
Reading frame       0 time  100.000   
lasttime 300


[ ... normal output until... ]


Continue writing frames from 44/traj.xtc t=100 ps, frame=10100      
Last frame        100 time  300.000    ->  frame  10200 time  300.000 ps     
Reading frame       0 time  100.000   
lasttime 300

Continue writing frames from 45/traj.xtc t=100 ps, frame=10201      
Last frame        100 time  300.000    ->  frame  10300 time  298.000 ps     
Reading frame       0 time  100.000   
lasttime 300
Reading frame       1 time  102.000   
Continue writing frames from 46/traj.xtc t=102 ps, frame=10302      
Last frame        100 time  300.000    ->  frame  10400 time  298.000 ps     
Reading frame       0 time  100.000   
lasttime 300
Reading frame       1 time  102.000   
Continue writing frames from 47/traj.xtc t=102 ps, frame=10402      
Last frame        100 time  300.000    ->  frame  10500 time  298.000 ps     
Reading frame       0 time  100.000   
lasttime 300
Reading frame       2 time  104.000   
Continue writing frames from 48/traj.xtc t=104 ps, frame=10502      
Last frame        100 time  300.000    ->  frame  10600 time  300.000 ps     
Reading frame       0 time  100.000   
lasttime 300
Reading frame       2 time  104.000   
Continue writing frames from 49/traj.xtc t=104 ps, frame=10601      
Last frame        100 time  300.000    ->  frame  10690 time  282.000 ps     
Reading frame       0 time  100.000   
lasttime 300
Reading frame       3 time  106.000   
Continue writing frames from 4/traj.xtc t=106 ps, frame=10700      
Last frame        100 time  300.000    ->  frame  10790 time  286.000 ps     
Reading frame       0 time  100.000   
lasttime 300
Reading frame       3 time  106.000   
Continue writing frames from 50/traj.xtc t=106 ps, frame=10798      
Last frame        100 time  300.000    ->  frame  10890 time  290.000 ps     
Reading frame       0 time  100.000   
lasttime 300

[ ... more drifting the first frame read until ... ]

Reading frame      30 time  160.000   
Continue writing frames from 99/traj.xtc t=160 ps, frame=15290      
Last frame        100 time  300.000    ->  frame  15360 time  300.000 ps     
Reading frame       0 time  100.000   
lasttime 300
Reading frame      30 time  160.000   
Continue writing frames from 9/traj.xtc t=160 ps, frame=15361      
Last frame        100 time  300.000    ->  frame  15430 time  298.000 ps     

Last frame written was 15431, time 300.000000 ps

===================================================================


==========================================================
Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne, Switzerland
http://ludwig-sun1.unil.ch/~mcuendet
==========================================================