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<title>Ghemical User Documentation - Geometry Optimization (Molecular Mechanics)</title>
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<h1>2.1.4 Geometry Optimization</h1>
<p>The Geometry Optimization tool will attempt to change the geometry of
the current molecule into the lowest energy conformation. To activate this
tool, right-click on the view window, select Compute from the popup menu,
and then click on Geometry Optimization.</p>
<img src="images/geometry_optimization_select.png" width="495"
height="428"
alt="Screenshot of menu sequence to select geometry optimization.">
<p>A dialog box called Geometry Opimization will appear. The three textboxes
in the dialog box control when to end the geometry optimization. Typically
only advanced users should change these fields. The "Maximum number of steps:"
field represents the maximum number of iterations that should be performed
before stopping the optimization. The "Gradient cutoff:" field represents
how low the length of the gradient vector can be before the optimization
stops. The "Delta E Cutoff:" field represents the minimum change in potential
energy between steps. Each of these checks can be disabled by unchecking
the checkbox to the left of each field.</p>
<img src="images/geometry_op_dialog.png" width="336" height="194"
alt="Screenshot of the geometry optimization dialog box.">
<p> Click on Ok to start the optimization. The conformation of the molecule
will change slightly at each step. In the log box, rows of text will
be printed. The first column indicates the step in the optimization currently
being executed. The second column is the potential energy of the molecule
at that step (this number will hopefully decrease). The third column is length
of the gradient vector in the last step. The forth column is the change in
potential energy from the previous step to the current step. The last line
on the column indicates which termination condition caused the optimization
to stop. "the nsteps termination test was passed." means that the optimization
went though the maximum number of steps allowed. This typically means that
ghemical could find a more optimum geometry if the optimization was allowed
to run for longer. If an optimization terminates because of this, running
a second geometry optimization might further optimize the geometry. Ghemical
may also print "the grad termination test was passed." or "the delta_e termination
test was passed." if the optimization stopped because of either of those
conditions.</p>
<h3>Example</h3>
<p>This example shows the geometry optimization of cyclohexane. Initially
this molecule is planar and the bond lengths are not equal.</p>
<img src="images/cyclohexane_unoptimized.png" width="409" height="426"
border="0"
alt="Screenshot of cyclohexane before geometry optimization.">
<p>A geometry optimization with the standard parameters is run. The optimization
stops at step 175 because the change in potential energy (delta_e) is below
1x10-7.</p>
<br>
<h4>Geometry Optimization log box example</h4>
<kdb>
Starting Geometry Optimization (molecular mechanics, engine = mm1_eng_exp1 : the default engine).
Cycle Energy Gradient Step Delta E
0 34064.44003 1.3967e+05 1.7976e-01 **********
1 20986.58834 1.3858e+05 2.0000e-01 1.3078e+04
2 5039.47883 6.6726e+04 3.4326e-01 1.5947e+04
3 3452.48739 3.5081e+04 5.8809e-02 1.5870e+03
[snip]
219 3.71368 3.0765e-01 2.1412e-06 3.1535e-07
220 3.71368 2.3451e-01 6.3032e-07 6.7052e-08
the delta_e termination test was passed.
</kdb>
<br>
<p>After optimization the cyclohexane molecule is now in the chair conformation
with all C-C bond lengths equivalent.</p>
<img src="images/cyclohexane_optimized.png" width="409" height="427"
alt="Screenshot of cyclohexane after MM1 geometry optimization.">
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