AMBER Archive (2005)

Subject: AMBER: runtime error in sander?

From: Dave S Walker (dswalker_at_darkwing.uoregon.edu)
Date: Tue May 31 2005 - 12:07:13 CDT

Hello all. I wrote a simple script to govern the simulation of about a
dozen different systems; most of them ran fine but for a few of them I
started getting this type of message:

endfile: truncation failed in endfile
apparent state: unit 6 named outfiles/ctcdcemd2.o
lately writing sequential formatted external IO

The output file, a 1ns continuation from a prior 2ns simulation that ran
smoothly, didn't appear to write output on all the 50ps increments it was
supposed to:

 grep NSTEP outfiles/ctcdcemd2.o
 NSTEP = 550000 TIME(PS) = 2550.000 TEMP(K) = 298.04 PRESS = 0.0
 NSTEP = 600000 TIME(PS) = 2600.000 TEMP(K) = 304.87 PRESS = 0.0
 NSTEP = 650000 TIME(PS) = 2650.000 TEMP(K) = 298.34 PRESS = 0.0
 NSTEP = 700000 TIME(PS) = 2700.000 TEMP(K) = 301.14 PRESS = 0.0
 NSTEP = 800000 TIME(PS) = 2800.000 TEMP(K) = 301.20 PRESS = 0.0
 NSTEP = 850000 TIME(PS) = 2850.000 TEMP(K) = 301.09 PRESS = 0.0
 NSTEP = 900000 TIME(PS) = 2900.000 TEMP(K) = 300.27 PRESS = 0.0
 NSTEP = 950000 TIME(PS) = 2950.000 TEMP(K) = 297.88 PRESS = 0.0

This may have something to do with the fact that for this simulation I'm
collecting coordinate/velocity information where for the first 2ns I
wasn't, but I'm not sure how to go about fixing these problems (that I
suspect are somehow related). Any help would be greatly appreciated.

dsw
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