[gmx-users] A water molecule can not be settled........

[David van der Spoel]

On Fri, 2003-07-04 at 14:26, Luca Mollica wrote:
> Dear users,
> 
> I have a problem running a double-precision simulation(all-bonds 
> restrained, 500 ps) using the latest version of GROMACS(implemented on 
> Linux SUSE 8.2).

What kind of hardware? Is it an Athlon processor? 

> After 360.288 ps, the simulation stopped and shell showed me the 
> following error message:
> 
> 
>  > 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.
>  > Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]
> 
> 
> Checking .log file, I've found the following message:
> 
> 
>  > t = 360.288 ps: Water molecule starting at atom 23951 can not be
>  > settled.
>  > Check for bad contacts and/or reduce the timestep.Wrote pdb files 
> with > previous and current coordinates
>  > Grid: -2147483648 x -2147483648 x -2147483648 cells
>  > Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]
> 
> 
> I've controlled the latest step with VMD, but the position of the 
> indicated water molecule is not ambiguos or "strange"(box borders or too 
> close to the protein, e.g), and no triclinic boxes were selected, but a 
> cubic box (8 A)* (8 A)* (8 A).
> 
> Could anyone kindly provide me some explanations of what could be 
> happened and a suitable solution for my problem ????
> 
> Thank you very much in advance
> 
> Luca Mollica
> 
> 
> 
> 
> 
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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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