Re: pairlist i_upper mismatch!

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Nov 20 2008 - 09:03:56 CST

The first thing to do would be to identify which atoms have non-unique
coordinates, figure out why they do, and correct the coordinates; I'm
not aware of any cases of non-unique coordinates triggering the error
you encountered, but the coordinates need to be fixed regardless...

Best,
Peter

Diego Alejandro Vargas wrote:
> 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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