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

[David]

On Sun, 2004-02-22 at 18:28, Wei Fu wrote:
> Hi, all
> 
>     I do MD simulation with rectangular pbc box, while the simulation
> crashes with the following error:

maybe too tight pressure coupling. which gromacs?

> _________________________________________________________________
> ^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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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