[gmx-users] mdrun errors out

Peter C. Lai sirmoo at cowbert.2y.net
Tue Aug 13 20:22:26 CEST 2002

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.

if anyone is interested.


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

More information about the gromacs.org_gmx-users mailing list