[gmx-users] mdrun errors out

[Peter C. Lai]

hi folks,
I pretty much used the "Getting started" section as a template
for setting up the mdrun. I solvated my protein, minimized,
and tried to mdrun. The first indication of trouble is lots of:

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.

It then quits with:
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]

If I change the ns_type to SIMPLE, it claims that twinneighbor
searching using simple algorithm is not implemented.

other notes: i used genconf to build the rectangular box. hasn't
given me any issues during minimization, only when trying to mdrun.

http://cowbert.2y.net/~sirmoo/yale/md/dev/200208131320/pr.mdp
if anyone is interested.

thanks,
pete

-- 
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
http://cowbert.2y.net/