j-ice – tutorial: build up a crystal -...

J-ICE – Tutorial: Build up a CRYSTAL - 1

P. Canepa - University of Kent – Torino -19th Jan 11

AIM: Build (from scratch) a CAFFEINE’s crystal and film

1 Look up on the web for caffeine PDB’s or XYZ’s file

2 Load it up on J-ICE

3 Apply crystal (or film) build’s procedure on J-ICE

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J-ICE – Tutorial: Build up a CRYSTAL - 2

Click on the checkBox

Start Procedure 1

Follow the procedure to build

3D, 2D and 1D objects

2

Having imported the desired molecule

P. Canepa - University of Kent – Torino -19th Jan 11 2  

J-ICE – Tutorial: Build up a CRYSTAL - 3

Set periodicity and perhaps space

group info 1

P. Canepa - University of Kent – Torino -19th Jan 11 3  

Enter cell parameters

2

Create Structure

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J-ICE – Tutorial: Build up a CRYSTAL - 4

P. Canepa - University of Kent – Torino -19th Jan 11 4  

A 3D objects: CRYSTAL

J-ICE – Tutorial: Build up a CRYSTAL - 5

P. Canepa - University of Kent – Torino -19th Jan 11 5  

A 2D objects: FILM

J-ICE – Tutorial: Build up a CRYSTAL - 5

P. Canepa - University of Kent – Torino -19th Jan 11 6  

A 2D objects: FILM

J-ICE – Tutorial: UFF optimizer

P. Canepa - University of Kent – Torino -19th Jan 11 7  

Imagine having build a new polymer ….

Pre-geometry optimization for a better stating point