[gmx-users] trjcat finds different spacing among trajectories

[Giuseppina La Sala]

Yes, gmxcheck gives me the time range that I expect for all my part*.xtc. I'm an pretty sure that the files are not corrupted. 
Infact I run the same command in the cluster were I performed the simulation (and not in my local machine as previously) and this time everything went well without problems.
It could be a problem of gromacs versions (cluster 4.6.3 and local machine 4.6.5) or... I don't know! 
Thanks for the replies!

Cheers

Josephine
     
________________________________________
Da: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] per conto di Christopher Neale [chris.neale at alum.utoronto.ca]
Inviato: venerdì 2 maggio 2014 21.00
A: gmx-users at gromacs.org
Oggetto: Re: [gmx-users] trjcat finds different spacing among trajectories

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?

Cheers

Josephine


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