Hi!<br><br>
<div><span class="gmail_quote">On 8/23/06, <b class="gmail_sendername">Marc Charendoff</b> <<a href="mailto:mcharend@sbcglobal.net">mcharend@sbcglobal.net</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">With Giovanna's help I was able to complete a grompp<br>run on my system. I did, however get a warning:<br>
<br>WARNING 1 [file "topol.top", line 12]:<br>Bad box in file Complex.GRO<br>Generated a cubic box 20.000 x 1.445 x 1.830</blockquote>
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<div>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? </div><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">What does this mean? Line 12 refers to one of my<br>complex molecules under the [molecule] header in this<br>
.top file.<br><br>When I attempt an energy minimization with the<br>resulting .tpr file I get:<br><br>Steepest Descents:<br> Tolerance (Fmax) = 1.00000e+00<br> Number of steps = 200<br>Warning: 1-4 interaction between 1 and 4 at distance
<br>3.024 which is larger than the 1-4 table size 1.000 nm<br>These are ignored for the rest of the simulation<br>This usually means your system is exploding,<br>if not, you should increase table-extension in your<br>mdp file
<br><br>... and the system proceeds to explode. What is this<br>warning really saying? What specifically do I need to<br>check, and is the bad box warning contributing to the<br>1-4 interaction problem?</blockquote>
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<div>often when the system explodes it has something to do with bad box construction. in any case, it is worth checking those measures. </div>
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Guidance Appreciated,<br><br>Marc</blockquote>
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<div>hope it helps,</div>
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<div>best wishes,</div>
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<div>Giovanna</div><br> </div>