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

[mu xiaojia]

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."


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
>
>