[gmx-users] I'm really stupid; BSD errors

Peter C. Lai sirmoo at cowbert.2y.net
Sat Aug 24 04:50:50 CEST 2002

Doh, I really ought to be slapped around for this one.
I built (and even uploaded to gromacs.org!) a build of 3.1.4
on FreeBSD-4.6.1 running on a K6-2 400. I posted earlier about
errors on mdrun. I finally decided to run the water and speptide systems
using step-by-step getting started instructions. They break!
On the water run, it has issues with pbc:

Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         NaN,          NaN,          NaN}
            Box[    1]={         NaN,          NaN,          NaN}
            Box[    2]={         NaN,          NaN,          NaN}
         Can not fix pbc.

On the speptide run, it throws the notorious 
Fatal error: ci = -2147483616 should be in 0 .. 159 [FILE nsgrid.c, LINE 210]
during minimization (and minimization with neighbor searching set to simple
makes the energies blow up to NaN).

I am thinking this is a compatibility error in the way bsd handles the
assembly loops. I built with --disable-x86-asm and the 2 tutorials work

Any other thoughts on this?

Peter C. Lai
University of Connecticut
Dept. of Molecular and Cell Biology | Undergraduate Research Assistant
Yale University School of Medicine
Center for Medical Informatics | Research Assistant

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