I’m running a 100ns MD simulation in 20ns intervals.
Up to 80ns pmemd.MPI produced the expected outputs and no error messages. I tested all trajectories and all appear to be fine.
Running the last interval 80ns-100ns I get the following error message repeatedly, which I assume has to do with the 80ns.rst file
This has occurred in the past sporadically and the way I dealt with the problem was to repeat the earlier interval (say 60-80ns) produce a new restart file and try again. Obviously not the best way to deal with the problem.
production Agam(3n7h-DEET:Dimer)
&cntrl
imin=0,irest=1,ntx=5,
nstlim=10000000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=2.0,
ntpr=5000, ntwx=5000,
ntt=3, gamma_ln=2.0, ig=-1,
ioutfm=1,
temp0=300.0,
/
Note: ig = -1. Setting random seed based on wallclock time in microseconds
and disabling the synchronization of random numbers between tasks
to improve performance.
| ERROR: I could not understand line 21122
112.1412192 403.0270264 138.5130746
Any suggestions regarding how to deal with this problem without repeat the earlier interval MD will be most welcome.
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Received on Mon Mar 16 2015 - 13:30:03 PDT
