[gmx-users] mdrun

David van der Spoel spoel at xray.bmc.uu.se
Fri Jan 10 15:42:03 CET 2003

On Fri, 2003-01-10 at 11:36, Outi Maija Salo wrote:
> Hi!
> What could be the problem with my mdrun if it collapses after the
> beginning and informs like this:
> Warning: Only triclinic boxes with the first vector parallel to the x-axis
> and t
> he 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.

You have very large forces for some reason. Is this in the beginning of
the run? THen you need to do more minimization. Do also check whether
you have periodic bondary problems.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 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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