[gmx-users] mdrun problems

[Scott Classen]

Hello GROMACS Users,
I am attempting to perform MD on a small molecule in a box of DMSO and 
after a few cycles of the simulation my log file starts growing very 
rapidly (Ikilled the job when my log file ballooned to 1GB). The file 
is mostly full of lines such as these:

Correcting invalid box:
old box (3x3):
    old box[    0]={-1.47359e+04,  0.00000e+00, -0.00000e+00}
    old box[    1]={ 0.00000e+00, -1.47827e+04, -0.00000e+00}
    old box[    2]={ 0.00000e+00,  1.18314e+09, -1.58862e+04}
new box (3x3):
    new box[    0]={-1.47359e+04,  0.00000e+00, -0.00000e+00}
    new box[    1]={ 0.00000e+00, -1.47827e+04, -0.00000e+00}
    new box[    2]={ 0.00000e+00,  1.18316e+09, -1.58862e+04}
Correcting invalid box:
old box (3x3):
    old box[    0]={-1.47359e+04,  0.00000e+00, -0.00000e+00}
    old box[    1]={ 0.00000e+00, -1.47827e+04, -0.00000e+00}
    old box[    2]={ 0.00000e+00,  1.18316e+09, -1.58862e+04}
new box (3x3):
    new box[    0]={-1.47359e+04,  0.00000e+00, -0.00000e+00}
    new box[    1]={ 0.00000e+00, -1.47827e+04, -0.00000e+00}
    new box[    2]={ 0.00000e+00,  1.18317e+09, -1.58862e+04}
Correcting invalid box:
old box (3x3):
    old box[    0]={-1.47359e+04,  0.00000e+00, -0.00000e+00}
    old box[    1]={ 0.00000e+00, -1.47827e+04, -0.00000e+00}
    old box[    2]={ 0.00000e+00,  1.18317e+09, -1.58862e+04}


Any ideas what I may be doing wrong?
Thanks in advance,
Scott

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   Scott Classen, Ph.D.
   ACS Postdoctoral Fellow
   Department of Molecular & Cell Biology
   University of California, Berkeley
   237 Hildebrand Hall #3206
   Berkeley, CA 94720-3206
   LAB 510.643.9491
   FAX 510.643.9290
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~