[gmx-users] why gmx can not minimize the sio2?

[Tsjerk Wassenaar]

gmx can not minimize the sio2 because YOU did something wrong somewhere.
(topology, infiniteness of the system, box, solvent)

Tsjerk

On 3/15/07, zzhwise1 <zzhwise1 at 163.com> wrote:
> hi all!
>     recently,i configuratued a sio2 base!
> but when i minimized it in gmx,it was wrong! and show the follow messeage!
>  -------------------------------------------------------
>
> Program mdrun, VERSION 3.3.1
>
> Source code file: nsgrid.c, line: 226
>
>
>
> Range checking error:
>
> Explanation: During neighborsearching, we assign each particle to a grid
>
> based on its coordinates. If your system contains collisions or parameter
>
> errors that give particles very high velocities you might end up with some
>
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
>
> put these on a grid, so this is usually where we detect those errors.
>
> Make sure your system is properly energy-minimized and that the potential
>
> energy seems reasonable before trying again.
>
>
>
> Variable ci has value -2147483648. It should have been within [ 0 .. 288 ]
>
> Please report this to the mailing list (gmx-users at gromacs.org)
>
> -------------------------------------------------------
>
> and i do not know why! for all the coordinates are right ,and i determined
> the O!
> can anyone help me?
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623