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

mu xiaojia muxiaojia2010 at gmail.com
Thu Apr 4 02:25:48 CEST 2013

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

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



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