Hi,
Unfortunately such corruption is possible and can result from things
like disk IO problems. With ASCII trajectories this meant all frames
after the corruption were almost always lost. Fortunately the NetCDF
format is robust enough so that corruption of a frame does not
necessarily result in corruption of subsequent frames. To process your
trajectory and avoid corrupt frames you can use the 'skipbadframes'
option of 'check', e.g.
trajin mytraj.nc
check skipbadframes .1,2
trajout nobadframes.nc
You may want to replace the mask '.1,2' with any atoms of interest to
ensure you are checking for corruption beyond the first two atoms.
Hope this helps,
-Dan
On Thu, Mar 19, 2015 at 9:46 AM, Jacopo Sgrignani <sgrigna.gmail.com> wrote:
> Dear Jason
> I got this error:
> Warning: Frame 511 coords 1 & 2 overlap at origin; may be corrupt
> I've never had this message before, I'm running simulations with the same
> input file and they work well.
>
> Jacopo
>
>
> 2015-03-19 16:26 GMT+01:00 Jason Swails <jason.swails.gmail.com>:
>
>> On Thu, 2015-03-19 at 15:20 +0100, Jacopo Sgrignani wrote:
>> > Dear all
>> > I'm trying to analyse a file of a trajectory (90ns) for a quite big
>> system
>> > (380000 atoms), however after 316 frames it starts to be corrupted and
>> > I'm unable to analyse it.
>>
>> What do you mean "corrupted"? Some kinds of corruption (e.g., if one
>> frame is corrupted due to some kind of I/O issue) result in a trajectory
>> where you can just skip over a frame. Other kinds of corruption (like
>> when a file is truncated) have lost information in a way that cannot be
>> recovered.
>>
>> Exact input and output will give us a better idea of what is going on
>> than just calling it broken or corrupt.
>>
>> There are some things you can look at yourself to figure some things
>> out. For instance, 380,000 atoms require 3x380,000=1.4M floating point
>> numbers for each frame. A 32-bit (4 byte) single precision float means
>> each frame should take *roughly* 4*1.4M/1024^2=4.34MB. If your file is
>> around 1.3 GB, then it only has about 316 frames worth of information at
>> best.
>>
>> All the best,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Mar 19 2015 - 21:30:03 PDT
