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

Marc Charendoff mcharend at sbcglobal.net
Wed Aug 23 03:06:56 CEST 2006

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

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? 

Guidance Appreciated,


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