This notebook contains a tutorial to perform MD simulations of an Octamethyl Silsesquioxane molecule with NAMD and the AMBER force field

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Table of Contents

Octa-methyl Silsesqioxane
Interpolation of Structure factors Working with python scripts View/Edit the contents on an ASCII file

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Examples of HTML and Markdown syntax</br>

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Octa-methyl Silsesqioxane (mPOSS)

The mPOSS molecule is composed of a cubic cage where silicon atoms occupy the cube vertices, and oxygen atoms are located in the cube edges (see below figure). Thus, each Si atom has a tetrahedral coordination to three O atoms and one methyl group. Methyl substitution by other chemical species makes POSS molecules highly versatile, with applications as organic solvents, polymer dispersants, catalysts, nanocomposites, diodes, and many other uses. In particular, mPOSS has found application as a coating for carbon fibers and low-dielectric films.

mPOSS molecule composed of Si (yellow), O (red), C (cyan), and H (grey) atoms. Nine different chains of consecutive O-Si-C-H covalent bonds can be constructed for each methyl group, due to the three different oxygen and hydrogen atoms that can be selected at the extremes of the chain.

mPOSS molecule non-vibrational degrees of freedom are restricted to dicrete rotational diffusion of the methyl groups (-CH3). In the AMBER force field the barrier to rotation is described by a dihedral 4-body term.

$V(\phi)=K[1+cos(3\phi)]$
Where $\phi$ is the dihedral angle defined by one of the nine combinations that can be formed with the four linked atoms O, Si, C, and H.

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Working with python scripts

All the fitting functions, settings, and tools can be carried out via a script in lieu of the graphical interface. In fact, there are complex fitting functions (like DSFinterp1DFit) that can only be run through a script.

Scripts are written in the python language. Any text editor can be used but for convenience, we will use the script editor available in MantidPlot. It has the advantage that all algorithms are automatically loaded into the namespace, thus simplifying the coding. The script editor is opened from the View menu: View $\rightarrow$ Script Window:

The script window has an upper pannel to write your code, and a lower pannel where output is printed.

Commands in the editor are executed from the Execute menu: Execute $\rightarrow$ Execute all. There's also the option to execute only the commands that are higlighted via Execute $\rightarrow$ Execute selection:

In the output panel, only two and three are printed. Notice also the green arrow indicating the last line in the script that was executed.

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View/Edit the contents on an ASCII file

For those not familiar with the Linux operating system, we enumerate here a few ways to view and/or edit an ASCII file:

1 File is shown in the terminal:

2 File is shown in a separate window

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Markdown Syntax Examples

local link: link</br> remote link: http://ambermd.org font face="courier new"
$$S_{model}(Q,E)=A(Q)\cdot S_{elastic}(E) + B(Q)\cdot S_{simulation}(Q,E)\otimes S_{elastic}(E) + C(Q)+D(Q)\cdot E$$

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