From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Apr 12 2018 - 15:28:31 CDT
Hello
I am carrying out with namd2.12 a FEP for Unbound ligand in water (as a
preliminary for ligand-protein complex) using 10 segments frwd and 10 back,
for a total 400 windows frwd and same back.
Segment back-02 has already completed. Out of all other running, frwd-09
crashed at step 54,000 of first window
colvars: The restart output state file will be "frwd-09.colvars.state".
> colvars: The final output state file will be "frwd-09_0.colvars.state".
> FEP: RESETTING FOR NEW FEP WINDOW LAMBDA SET TO 0.8 LAMBDA2 0.8025
> FEP: WINDOW TO HAVE 100000 STEPS OF EQUILIBRATION PRIOR TO FEP DATA
> COLLECTION.
> FEP: USING CONSTANT TEMPERATURE OF 300 K FOR FEP CALCULATION
> PRESSURE: 0 -368.104 569.455 -539.08 569.454 -304.251 -1415.15 -539.08
> -1415.15 181.994
> GPRESSURE: 0 -260.121 387.556 -718.786 295.641 -123.294 -1219.32 -365.275
> -1092.12 269.401
> ETITLE: TS BOND ANGLE DIHED
> IMPRP :
> ...................................
> .....................................
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 53500
> WRITING COORDINATES TO DCD FILE frwd-09.dcd AT STEP 53500
> WRITING COORDINATES TO RESTART FILE AT STEP 53500
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 53500
> FINISHED WRITING RESTART VELOCITIES
> colvars: Synchronizing (emptying the buffer of) trajectory file
> "frwd-09_0.colva
> rs.traj".
> colvars: Writing the state file "frwd-09.colvars.state".
> WRITING COORDINATES TO DCD FILE frwd-09.dcd AT STEP 54000
> WRITING COORDINATES TO RESTART FILE AT STEP 54000
> FATAL ERROR: Unable to open binary file frwd-09.coor: File exists
> [0] Stack Traceback:
>
I had never encountered such a problem and wonder whether this stems from
the code or the cluster (each FEP on one node, 36 core, NextScale).
frwd-09.coor (which is bincoor) has normal size (did not try with psf/vmd),
while, curiously, frwd-09.dcd and frwd-dcd.BAK were generated alongside
back-09.fepout and back-09.fepout.BAK, as if the dcd and fepout files had
been present initially (but they were not). Also, no anomaly can be seen in
frwd-09.namd and frwd-09.job.
At any event, I am deleting all generated frwd-09 files and restarting from
scratch in the hope that it was a non systematic error.
thanks for advice
francesco pietra
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