On 8/23/06, Marc Charendoff <[EMAIL PROTECTED]> 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,
Giovanna
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