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

[Wei Fu]

Hi, David,

   I check the output file and found it still generates the same error:
^Mstep 1380, will finish at Sun Feb 22 19:17:15 2004
Wrote pdb files with previous and current coordinates
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[    0]={         nan,          nan,          nan}
         Box (3x3):
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
         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 *****
***** MPI-error in rank 0 Routine MPI_Abort : Terminating after call to
MPI_Abort *****

So, it generates the step*.pdb file.

look forward to your help!

Wei