[gmx-users] trjcat finds different spacing among trajectories

[Mark Abraham]

/waves his magic wand... You were on a FAT32 file system with 2GB file size
limits and about 350ns reaches that?

Mark


On Fri, May 2, 2014 at 11:44 PM, Giuseppina La Sala <
giuseppina.lasala2 at unibo.it> wrote:

> 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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