[gmx-users] g_rms on large (1.5 GB) trr file

[K.A. Feenstra]

dr.horsfield at physics.org wrote:
> 
> Hi,
> 
> I have been using g_rms to monitor the progress of a job that has been
> running for some weeks, and have never had any trouble until now. I now
> get the error:
> 
>   trn version: GMX_trn_file
>   Reading frame    1460 time 2920.000   There were 4 inconsistent shifts.
>   Check your topology
>   Segmentation fault (core dumped)
> 
> I assume the problem is related to the size of the trr file (1.5GB),
> though I am not sure why this should be the case.

Sorry for the late response. Something just occurred to me. The filesize
here shouldn't matter: 1.5GB is nothing special (2.0GB *is*). But, what
can happen on occasion for unexplained reasons is that a part of a file
can go missing. My guess is that this only happens when writing to NFS
(ie over the network), possibly due to a packet loss. This ofcourse 
should never happen, it is actually very rare, but we had one definite
instance of it once in Groningen.

So, possibly your file is corrupt. You can check this using gmxcheck,
which uses slightly lower-level reading routines than g_rms (and other
tools) does. If you really need to read the rest of your trajectory
(and I assume you would), the only solution is to search the file after
the corrupted part for the Gromacs magic number, which occupies the
first 4 bytes (if I am correct) of each frame in the trajectory. If
you  work out the statistics, on average it should only occur once
every 4 Tera-B or so, so it is unlikely to occur by chance. IIRC the
number is '1995' (but, check). Then, from the magic number (including
it), you can read onwards...

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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