[gmx-users] trjcat finds different spacing among trajectories

Christopher Neale chris.neale at alum.utoronto.ca
Fri May 2 21:00:56 CEST 2014

When you run gmxcheck on md_0_1.part0014.xtc and md_0_1.part0015.xtc separately, what start and end times do you get for each of the two files?
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Giuseppina La Sala <giuseppina.lasala2 at unibo.it>
Sent: 02 May 2014 11:30
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] trjcat finds different spacing among trajectories

Hi GMX-Users,

I'm trying to use trjcat command to join very large trajectories:
trjcat -f md_0_1.part*.xtc -s md_0_1.tpr -o all.xtc

but I found this error while gmx was reading the frames:

 Reading frame    2000 time 351750.000    ->  frame  70350 time 351750.000 ps ->  frame  70430 time 352150.000 ps
WARNING: Frames around t=352190.000000 ps have a different spacing than the rest,
might be a gap or overlap that couldn't be corrected automatically.
Reading frame       0 time 396625.000
lasttime 352190

Continue writing frames from md_0_1.part0015.xtc t=396625 ps, frame=70439
Reading frame       1 time 396630.000    ->  frame  70440 time 396630.000 ps

I run gmxcheck and it didn't give me any warnings.
The version of Gromacs that I'm using is 4.6.3.

Does anyone know what could be the root of the problem?



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