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Instruction Modelling

The document provides instructions for using the AMS software to draw, optimize, analyze, and visualize molecular structures. It describes how to: 1. Draw a molecule by selecting atoms and bonds and optimize the force field to determine potential energy. 2. Perform rotations, translations, save images, and select multiple atoms for manipulations like rotations and measuring distances or angles between atoms. 3. Optimize molecular structures according to requirements and view results like total bonding energy, energy graphs, and orbital information. 4. Visualize electron density, molecular electrostatic potential maps, and movie simulations of electronic energies.

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Ngoc Nguyen
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© © All Rights Reserved
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Download as DOCX, PDF, TXT or read online on Scribd
19 views

Instruction Modelling

The document provides instructions for using the AMS software to draw, optimize, analyze, and visualize molecular structures. It describes how to: 1. Draw a molecule by selecting atoms and bonds and optimize the force field to determine potential energy. 2. Perform rotations, translations, save images, and select multiple atoms for manipulations like rotations and measuring distances or angles between atoms. 3. Optimize molecular structures according to requirements and view results like total bonding energy, energy graphs, and orbital information. 4. Visualize electron density, molecular electrostatic potential maps, and movie simulations of electronic energies.

Uploaded by

Ngoc Nguyen
Copyright
© © All Rights Reserved
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
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Freija 10/10

Open AMS
Create directory : on top panel : file -> new directory
On panel, choose scm -> new input
Draw c2h5oh by choosing carbon and atom
Add hydrogen: click “atom” on panel, choose “add hydrogen”
Optimize the force field for “suitable potential energy” , click icon “bánh răng cưa” phía
dưới bên phải and wait until it’s done

Rotate: 3 fingers pad


Rotate only plane: command+ 3 finger
Translate: shift+1finger

Save molecule photo: file -> save picture


Choose multiple atoms: shift click on atoms
Rotate chosen atoms: command + CLICK ON 1 ATOM TO rotate
Distance between atoms: click 1 atom and shift click another
Change distance: the bar on the bottom
Angle: click 1 atom and shift click 2 others
Dihedral angle: click 1 atom and shift click 3 others
IMPORTANT: only click pre-optimization after cliking on empty space to ensure optimization
for whole molecule not only chosen part
To see coordinate:
In AMS input window, choose “model on right panel” and choose coordinate
A table shows up all molecules with their coordinate.
 When change angle, these coordinate values change
To know which atom is which in the table:
Top panel, view – atom info – name

Do optimization:
Choose options according to the requirement or instructions, those are not mentiones ->
leave as default
Go to file -> save and name the file
Go the ams jobs window and go to job -> run
Double click on the running lines to open full running window, when it’s finshed, there will
be TERMINATION line and result is “bond energy”

Go to AMS job, choose file with .out, double click to open to see total bonding energy (in
summary part)

To see movie, go to AMS job, top left panel, choose scm -> movie to see electronic energy.
See additional result (energy from angle, etc) AMS job -> graph -> add graph -> choose
distance/angle and go back to graph -> distance, angle, dihedral
Alternatively, top panel, go to geometric info -> angle/distance

To see orbital level energy, in ams jobs, choose the file and click scm -> levels to see HOMO
LUMO
Label/ name the energy label by clicking on the “dash” and choose show label
To visualize the orbital, click and hold on the label

Visualize e density and other properties: in ams job, choose file, on top panel choose scm ->
view. On pop-up window, on top panel, choose properties -> density

To see molecular electrostatic potential map: in ams view, top panel, click add -> isosurface:
color. Then, on the ams view, at the bottom, the new line is created, choose density scf and
coulomb potential scf. To see the strength, tick the box “bar”

Freija 24/10
3 finger: xoay molecule
2 finger: zoom in
Do optimization with h2o2 and 1 more optimization with stricter requirements
 Scope: compare the dihedral angle between 2 molecules (must be no diff)

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