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 <muxiaojia2...@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
========================================
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