[gmx-users] corrupt trr file?

[David van der Spoel]

Samantha Kaye wrote:
> But the first file can't be successfully gmxcheck-ed, I get the precision error mentioned below.
ok, I see. You will have to truncate it after 4500 ps using trjconv -e 
or trjconv -trunc

> 
> 
> In message <44C504B8.2040101 at xray.bmc.uu.se> Discussion list for GROMACS users <gmx-users at gromacs.org> writes:
> 
>>Samantha Kaye wrote:
>>
>>>Yes using trjcat. It returns a magic number error.
>>
>>could this by chance be run on a 64 bit powerpc?
>>
>>If the two original files can be gmxcheck-ed then the catted file should 
>>be fine too.
>>
>>
>>>
>>>In message <44C4CA58.5080209 at xray.bmc.uu.se> Discussion list for GROMACS users <gmx-users at gromacs.org> writes:
>>>
>>>
>>>>Samantha Kaye wrote:
>>>>
>>>>
>>>>>Hi,
>>>>>
>>>>>Whenever I try to make a continuation file for my simulation I can generate a tpr file using tpbconv but I can't cat the ouput files together afterwards.
>>>>>
>>>>
>>>>did you use trjcat ?
>>>>
>>>>
>>>>
>>>>>When I run ">gmxcheck -f closed1122_unrest.trr" on the first trr file I get the following:
>>>>>
>>>>>
>>>>>Checking file closed1122_unrest.trr
>>>>>trn version: GMX_trn_file (single precision)
>>>>>Reading frame       0 time    0.000
>>>>># Atoms  189376
>>>>>Reading frame     910 time 4550.000   -------------------------------------------------------
>>>>>Program gmxcheck, VERSION 3.3
>>>>>Source code file: trnio.c, line: 66
>>>>>
>>>>>File input/output error:
>>>>>Can not determine precision of trn file
>>>>>-------------------------------------------------------
>>>>>
>>>>>
>>>>>I've tried generating the continuation file from an earlier frame but have the same problem always at frame 910.
>>>>>
>>>>>The file is over 2gb but as tpbconv runs without a problem I don't think that's the problem.
>>>>>
>>>>>Any suggestions?
>>>>>
>>>>>Thanks
>>>>>
>>>>
>>>>
>>>>-- 
>>>>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://folding.bmc.uu.se
>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>>_______________________________________________
>>>>gmx-users mailing list    gmx-users at gromacs.org
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>>>>
>>>
>>>
>>
>>-- 
>>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://folding.bmc.uu.se
>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>_______________________________________________
>>gmx-users mailing list    gmx-users at gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please don't post (un)subscribe requests to the list. Use the 
>>www interface or send it to gmx-users-request at gromacs.org.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
> 
> 


-- 
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://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++