pairlist i_upper mismatch!

From: Diego Alejandro Vargas (vardiego9_at_gmail.com)
Date: Wed Nov 19 2008 - 22:28:41 CST

Hi everybody,
I am trying to run an equilibration simulation for a protein in a water box
on an AMD64 Linux cluster with Rocks OS. The 10000 minimization steps run
well, but the equilibration simulation is crashing in the first time step
with the following error message:

TCL: Running for 500 steps
Warning: Not all atoms have unique coordinates.
PRESSURE: 0 -157.951 -29.8596 -16.0059 -29.8596 -77.2141 17.8006 -16.0059
17.8006 113.888
GPRESSURE: 0 -166.041 -53.081 15.1011 -39.8107 -82.785 19.326 8.98805 1.1757
126.742
ETITLE: TS BOND ANGLE DIHED
IMPRP
           ELECT VDW BOUNDARY MISC
KINETIC
            TOTAL TEMP TOTAL2 TOTAL3
TEMPAVG
    PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 0 403.8150 1229.3825 2078.1846
39.2413
    -467115.5621 99999999.9999 0.0000 0.0000
0.0000
99999999.9999 0.0000 99999999.9999 99999999.9999
0.0000
          -40.4258 -40.6949 1140720.0000 -40.4258
-40.6949

OPENING EXTENDED SYSTEM TRAJECTORY FILE
FATAL ERROR: pairlist i_upper mismatch!

Can anybody explain the meaning of "pairlist i_upper mismatch" to me? I
thought it'd be related to the pair list of atoms for which to calculate
non-bonded interactions, but most allusions to the error I found in the
mailing list had to do with problems with software/hardware interface or
running of NAMD binaries.

Note that I get the Warning: Not all atoms have unique coordinates. This
warning is not present in the log file for the minimization. Also, I believe
my cellViasVector dimensions are large enough (slightly over 1A of max-min
in each dimension). I generated my pdb and psf files with the automatic psf
generator and got no error messages. I inspected the resulting files along
with the .coor and .dcd files from the minimization on VMD and it looks
fine.

Let me know if you have any insight into the problem. Let me know if you
anything that may help.

Diego A. Vargas

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