[gmx-users] Re: cannot read frames out from trr files

[mu xiaojia]

Thanks Justin,

It never happens to my simulations before, is there anyway to figure out
what caused this corruption?  the log file and screen outputs didn't
mentioned any error message. I am wandering if it was caused by the
unstable super-cluster I am currently using, because on another
super-clusters, it never happened before.


On Wed, Apr 3, 2013 at 7:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/3/13 8:42 PM, mu xiaojia wrote:
>
>> Sorry for the typo, the last evidence"4) I also compared the generated
>> files' sizes, A = B in trr, edr , gro, cpt, if B crashes before reaching
>> 100ns, the size would **NOT*** be the same as A."
>>
>>
> You probably have a corrupted frame.  The simulation continued and the
> .trr file continued being written, so you see comparable file sizes.
>
> -Justin
>
>
>> On Wed, Apr 3, 2013 at 7:25 PM, mu xiaojia <muxiaojia2010 at gmail.com>
>> wrote:
>>
>>  Dear GMX users,
>>>
>>> I am not sure if someone has similar problems before. I cannot read half
>>> of the frames from trr file after md simulation, and I believe my
>>> simulation has already completed.
>>>
>>> I have finished simulations A and B with both gmx4.5.4 and gmx4.5.5. the
>>> only difference between A and B is they are npt simulations under
>>> different
>>> temperature (in mdp file, "ref_t" part )and such difference would not
>>> cause
>>> crash of the simulation. I have successfully finished A, everything looks
>>> perfect (frames can be successfully extracted), but for B, I could not
>>> extract last 70ns' frames from trr.
>>>
>>> 1) My command is like: mdrun_mpi -s -deffnm MD_A -cpi -append, because I
>>> am using super computer so the job will be restarted for multiple times.
>>>
>>> 2) both simulation are 100ns, both log files indicate that they have
>>> finished 100ns simulations. I checked my screen out put for B, whenever
>>> it
>>> restarted, the output on screen is correct and continuously ( something
>>> like: 100000000 steps, 100000.0 ps (continuing from step 95963500,
>>>  95963.5
>>> ps).
>>>
>>> 3) With gmxcheck, it looks that my B simulation only reached 29,7ns(which
>>> means only the first two restart simulation were recorded into trr, which
>>> log files are not saying in this way.)
>>> *
>>> *
>>> *For system A (the successful one), it shows*
>>>
>>> Reading frame       0 time    0.000
>>> # Atoms  72166
>>> Last frame     2000 time 100000.000
>>>
>>>
>>> Item        #frames Timestep (ps)
>>> Step           2001    50
>>> Time           2001    50
>>> Lambda       2001    50
>>> Coords         2001    50
>>> Velocities     2001    50
>>> Forces           0
>>> Box            2001    50
>>>
>>> *for system B (the failed one)*
>>>
>>> Reading frame       0 time    0.000
>>> # Atoms  72166
>>> Reading frame     500 time 25000.000
>>>
>>>
>>> Item        #frames Timestep (ps)
>>> Step           596    50
>>> Time           596    50
>>> Lambda         596    50
>>> Coords         596    50
>>> Velocities     596    50
>>> Forces           0
>>> Box            596    50
>>>
>>> 4) I also compared the generated files' sizes, A = B in trr, edr , gro,
>>> cpt, if B crashes before reaching 100ns, the size would be the same as A.
>>>
>>> I am wondering what was wrong with my trr file of B . I appreciate for
>>> any
>>> suggestions!
>>>
>>> Sincerely
>>>
>>> Xiaojia
>>>
>>>
>>>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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