[gmx-users] help!!! "can not fix pbc"

[Wei Fu]

Hi, all

    I do MD simulation with rectangular pbc box, while the simulation
crashes with the following error:
_________________________________________________________________
^Mstep 102950, will finish at Tue Feb 24 11:03:47 2004
^Mstep 102960, will finish at Tue Feb 24 11:03:48 2004
Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
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.
         Box (3x3):
         Box (3x3):
         Box (3x3):
            Box[    0]={         nan,          nan,          nan}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
......
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):
Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
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):
Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
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}
         Can not fix pbc.
            Box[    0]={         nan,          nan,          nan}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 218]
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 218]
***** MPI-error in rank 2 Routine MPI_Abort : Terminating after call to
MPI_Abort *****
***** MPI-error in rank 3 Routine MPI_Abort : Terminating after call to
MPI_Abort *****
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 218]
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 218]
***** MPI-error in rank 1 Routine MPI_Abort : Terminating after call to
MPI_Abort *****
_________________________________________________________________

I looked at the box size but at the last recorded step it is OK. No atom
is out of box. The protein structure looks good. How should I fix this
error? Any hints will be highly appreciated!!!

Wei