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

Luca Mollica mollica.luca at hsr.it
Fri Jul 4 15:26:02 CEST 2003

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).
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


Luca Mollica
Dulbecco Telethon Institute (Protein Structure Laboratory)
c/o Cellular and Molecular Neurobiology
DIBIT-HSR,Via Olgettina 58
20132 Milano (Italy)

Tel: 0039-02-26434824
Fax: 0039-02-26434813
E-mail: mollica.luca at hsr.it

DTI website: http://www.telethon.it/dti/

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