[gmx-users] Fatal error: XTC error

[David van der Spoel]

Erik Lindahl wrote:

> Hi,
>
> In short, it means that gromacs got a non-zero return code when using 
> the XTC routines to write to a file (probably your trajectory).
>
> This is almost certainly due to an I/O error. Common explanations 
> besides a full disk are:
>
> 1. Output file exceeds 2Gb on a non-largefile filesystem (e.g. NFSv2)
> 2. Your quota is full
> 3. Disk hardware error
> 4. Network error if you use NFS
>
> In theory it might also happen if you try to write coordinates that 
> involve "NaN", but if it happened during a run I think other routines 
> would have caught a severely crashing simulation first.
>
They don't have to be NaN, just big. In vacuum simulations where 
molecules evaporate you also get these problems. We can only use trr for 
our microsecond trajectories :(


> Cheers,
>
> Erik
>
> On Dec 5, 2005, at 3:03 PM, Rahul Karyappa wrote:
>
>> Dear all,
>>    I had started the MD run for 5ps(5000 steps) on my model. But 
>> after 490 steps of MD run it gave me following error:
>>
>> Fatal error: XTC error
>>
>> What is the reason for this? I checked the disk space but it is not 
>> full. PLease let me know about this. Thanking you in advance.
>>
>> Rahul Karyappa
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>
>
> -----------------------------------------------------------
> Erik Lindahl  <lindahl at sbc.su.se <mailto:lindahl at sbc.su.se>>
> Assistant Professor, Stockholm Bioinformatics Center
> Stockholm University, SE 106 91 Stockholm
> Phone: +46 8 5537 8564     Fax: +46 8 5537 8214
>
>
>
>
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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://xray.bmc.uu.se/~spoel
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