[gmx-users] help!!! "can not fix pbc"
Wei Fu
fuwei at adrik.bchs.uh.edu
Sun Feb 22 19:15:01 CET 2004
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
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