Hi all,
I am trying to run a simulation on peptide linked to APD-ribose (following tutorial advanced tut 1_orig). I was able to save the prmtop and inpcrd files. After performing heating, equilibration shows MPI_Abort process 0.
equil.out looks as below and says "wall clock was called"
Any suggestions? Recommended reading?
5. TIMINGS
--------------------------------------------------------------------------------
| Read coords time 0.00 ( 0.01% of Total)
| Calc gb radii 2.19 (20.49% of Gen B)
| Calc gb diag 4.24 (39.76% of Gen B)
| Calc gb off-diag 4.24 (39.75% of Gen B)
| Other 0.00 ( 0.01% of Gen B)
| Gen Born time 10.67 (100.0% of Nonbo)
| Nonbond force 10.67 (96.34% of Force)
| Bond/Angle/Dihedral 0.40 ( 3.64% of Force)
| Other 0.00 ( 0.02% of Force)
| Force time 11.07 (97.68% of Runmd)
| Verlet update time 0.26 ( 2.31% of Runmd)
| Other 0.00 ( 0.01% of Runmd)
| Runmd Time 11.34 (99.89% of Total)
| Other 0.01 ( 0.10% of Total)
| Total time 11.35 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
| Final Performance Info:
| -----------------------------------------------------
| Average timings for all steps:
| Elapsed(s) = 11.34 Per Step(ms) = 11.34
| ns/day = 7.62 seconds/ns = 11336.34
| -----------------------------------------------------
| Job began at 13:08:00.956 on 12/17/2014
| Setup done at 13:08:00.969 on 12/17/2014
| Run done at 13:08:12.305 on 12/17/2014
| wallclock() was called 22081 times
REALLY APPRECIATE ALL THE HELP !
-AG
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Received on Wed Dec 17 2014 - 12:00:02 PST
