[gmx-users] error while concatenating .xtc files

[David van der Spoel]

Alan Dodd wrote:
> I had a similar error yesterday, try writing the
> problem frames to pdb or something similarly readable.
>  I found that the frame I crashed at had been
> corrupted somehow, and the coordinates for a chunk of
> my system were all messed up - either way, you should
> be able to see the problem.  xtc  files seem to be a
> little more sensitive to glitches than the rest.
with 3.3 you could try to use trjconv to extract the second bit by 
giving the -b option, it may hop over the point where the file is broken.

> 
> --- manmohan singh <monu_bt at yahoo.com> wrote:
> 
> 
>>Hi there!
>>
>> 
>>I was wondering if one can reply me about error that
>>i
>>m getting.
>> while concatenating .xtc file having both solvent
>>and
>>protein following error is shown. 
>>
>>
>>
> 
> ============================================================================
> 
>>Continue writing frames from extend4ns.xtc t=2000
>>ps,
>>frame=4000
>>Reading frame     540 time 2270.000   Fatal error:
>>Magic Number Error in XTC file (read 43333021,
>>should
>>be 1995)
>>
> 
> ============================================================================
> 
>>but no error was obseverd while concatenating .xtc
>>file having only protein
>>
>>
>> Sincerely
>>
>>manmohan
>>
>>
> 
> ************************************************************************
> 
>>Manmohan Singh Gurjar
>>M.Sc.Biotechnology(IInd year)
>>School of Bioscience and Bioengineering
>>IIT Powai
>> Mumbai-400076
>>e-mail monu_bt at iitb.ac.in
>>       monu_bt at yahoo.com
>>mobile- 9819850822
>>
> 
> ************************************************************************
> 
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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
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