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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
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<title>Basic Molecular Mechanics Modelling</title>
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<body>
<h2> </h2>
<h1>2. User's Manual</h1>
<h1>2.1 Molecular Mechanics Modelling</h1>
<h1>2.1.1 Quick Start : modelling Ethanol</h1>
<p>This section covers the features required to build a simple molecule (Ethanol)
using ghemical.</p>
<h3>Step 1</h3>
<p>After starting ghemical you must open a new project. To do this, click
on the File menu and select "New"</p>
<img src="images/using_mm_01.png"
alt="A Screenshot of the creation of a new project.">
<h3>Step 2</h3>
<p>Select Draw from the toolbar on the left hand side. The Draw tool is the
method that all bonds and atoms are added with.</p>
<img src="images/using_mm_02.png"
alt="Screenshot of selecting the draw mouse tool in ghemical.">
<h3>Step 3</h3>
<p>Now begin to add atoms and bonds to your molecule. The default atom type
is carbon. To add a single atom to the molecule, single click on the location
you would like to put the atom. </p>
<img src="images/using_mm_03.png"
alt="Screenshot of the first atom being added to the molecule.">
<p> To draw a bond between two atoms, single left click on the first atom
in the bond, drag the mouse over to the second atom and then release the
mouse button. You may also create atoms and bonds at the same time by left
clicking on an existing atom, dragging the mouse to where you want to place
the second atom and then releasing the mouse button.</p>
<img src="images/using_mm_04.png" alt="Screenshot of two carbon atoms bonded together.">
<h3>Step 4</h3>
<p> Now that the carbon backbone is created, we can now add the missing oxygen
atom, and after this step we have all the heavy (non-Hydrogen) atoms ready.
To do this, we must first change the atom type from carbon to oxygen.
This is done selecting the periodic table button from the top toolbar.</p>
<img src="images/using_mm_05.png"
alt="Screenshot of Set Current Element toolbar button.">
<p> A dialog box of the periodic table will appear. To select an element,
simply click on the button corresponding to it. All further atoms drawn
on the molecule will be of this element until it is changed by the same
method. In this example, oxygen is selected.</p>
<img src="images/using_mm_06.png"
alt="Screenshot of the periodic table dialog box.">
<h3>Step 5</h3>
<p>In this step the additional oxygen atoms is added to the molecule in same way
the second carbon atom was added.</p>
<img src="images/using_mm_07.png"
alt="Screenshot of oxygen atom being added to the carbon atoms.">
<h3>Step 6</h3>
<p>Finally, the hydrogen atoms are added. This can be done (for simple organic
compounds) using an automated tool that will add hydrogen atoms (find popup-menu
item Build/Hydrogens/Add).</p>
<img src="images/using_mm_08.png"
alt="Screenshot of hydrogen atoms being added to the carbon atoms.">
<p>Alternatively, the hydrogen atoms can be added manually, as carbon and oxygen
atoms were added earlier. Now all atoms of an ethanol molecule are added.</p>
<img src="images/using_mm_09.png"
alt="Screenshot an ethanol molecule with all atoms added.">
<h3>Step 7</h3>
<p>Although the all the correct atoms and bonds are present, the molecule
is not in the most stable conformation. Ghemical can attempt to do this
for you using the Geometry Optimization tool (find popup-menu
item Compute/Geometry Optimization).</p>
<img src="images/using_mm_10.png"
alt="Screenshot of geometry optimization being started.">
<p>After running Geometry Optimization, the bond lengths, bond angles and
other structural features of the ethanol molecule are set in their ideal values
(according to the molecular mechanics force field used for geometry optimization).</p>
<img src="images/using_mm_11.png"
alt="Screenshot of an ethanol molecule.">
<p>You can also change the bond type by clicking on the "Set the current
bond type" button on the top tool bar. This button will launch a dialog
box that lets you select the bond type
from a list of single, double, triple and conjugated. All further bonds
that you create will be on the type that you select until you change the
bond type again. Conjugated bonds are drawn as a single solid tube with
a second dashed tube parallel to it. Double bonds and triple bonds are
drawn as two and three parallel tubes respectively.</p>
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