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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Received on Thu Mar 19 2015 - 09:00:05 PDT
