[gmx-users] Thanks to Giovanna! Now, exploding system . . .

MGiò magiofer at gmail.com
Wed Aug 23 08:55:34 CEST 2006


On 8/23/06, Marc Charendoff <mcharend at sbcglobal.net> wrote:
> With Giovanna's help I was able to complete a grompp
> run on my system. I did, however get a warning:
> WARNING 1 [file "topol.top", line 12]:
> Bad box in file Complex.GRO
> Generated a cubic box   20.000 x    1.445 x    1.830

are you sure this measures of your system box are correct? they look very
strange to me, indeed, have you a 20nm side of the box, and are the others
1.4 and 1.8?

What does this mean? Line 12 refers to one of my
> complex molecules under the [molecule] header in this
> .top file.
> When I attempt an energy minimization  with the
> resulting .tpr file I get:
> Steepest Descents:
>   Tolerance (Fmax)   =  1.00000e+00
>   Number of steps    =          200
> Warning: 1-4 interaction between 1 and 4 at distance
> 3.024 which is larger than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your
> mdp file
> ... and the system proceeds to explode. What is this
> warning really saying?  What specifically do I need to
> check, and is the bad box warning contributing to the
> 1-4 interaction problem?

often when the system explodes it has something to do with bad box
construction. in any case, it is worth checking those measures.

Guidance Appreciated,
> Marc

hope it helps,

best wishes,

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