j-ice – tutorial: build up a crystal -...
TRANSCRIPT
![Page 1: J-ICE – Tutorial: Build up a CRYSTAL - 1j-ice.sourceforge.net/oldwebpage/docs/01-Build-CRYSTAL.pdf · 2011-05-22 · J-ICE – Tutorial: Build up a CRYSTAL - 2 Click on the checkBox](https://reader033.vdocuments.mx/reader033/viewer/2022043016/5f38ecacc05edb773d0a1923/html5/thumbnails/1.jpg)
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
1
![Page 2: J-ICE – Tutorial: Build up a CRYSTAL - 1j-ice.sourceforge.net/oldwebpage/docs/01-Build-CRYSTAL.pdf · 2011-05-22 · J-ICE – Tutorial: Build up a CRYSTAL - 2 Click on the checkBox](https://reader033.vdocuments.mx/reader033/viewer/2022043016/5f38ecacc05edb773d0a1923/html5/thumbnails/2.jpg)
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
![Page 3: J-ICE – Tutorial: Build up a CRYSTAL - 1j-ice.sourceforge.net/oldwebpage/docs/01-Build-CRYSTAL.pdf · 2011-05-22 · J-ICE – Tutorial: Build up a CRYSTAL - 2 Click on the checkBox](https://reader033.vdocuments.mx/reader033/viewer/2022043016/5f38ecacc05edb773d0a1923/html5/thumbnails/3.jpg)
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
3
![Page 4: J-ICE – Tutorial: Build up a CRYSTAL - 1j-ice.sourceforge.net/oldwebpage/docs/01-Build-CRYSTAL.pdf · 2011-05-22 · J-ICE – Tutorial: Build up a CRYSTAL - 2 Click on the checkBox](https://reader033.vdocuments.mx/reader033/viewer/2022043016/5f38ecacc05edb773d0a1923/html5/thumbnails/4.jpg)
J-ICE – Tutorial: Build up a CRYSTAL - 4
P. Canepa - University of Kent – Torino -19th Jan 11 4
A 3D objects: CRYSTAL
![Page 5: J-ICE – Tutorial: Build up a CRYSTAL - 1j-ice.sourceforge.net/oldwebpage/docs/01-Build-CRYSTAL.pdf · 2011-05-22 · J-ICE – Tutorial: Build up a CRYSTAL - 2 Click on the checkBox](https://reader033.vdocuments.mx/reader033/viewer/2022043016/5f38ecacc05edb773d0a1923/html5/thumbnails/5.jpg)
J-ICE – Tutorial: Build up a CRYSTAL - 5
P. Canepa - University of Kent – Torino -19th Jan 11 5
A 2D objects: FILM
![Page 6: J-ICE – Tutorial: Build up a CRYSTAL - 1j-ice.sourceforge.net/oldwebpage/docs/01-Build-CRYSTAL.pdf · 2011-05-22 · J-ICE – Tutorial: Build up a CRYSTAL - 2 Click on the checkBox](https://reader033.vdocuments.mx/reader033/viewer/2022043016/5f38ecacc05edb773d0a1923/html5/thumbnails/6.jpg)
J-ICE – Tutorial: Build up a CRYSTAL - 5
P. Canepa - University of Kent – Torino -19th Jan 11 6
A 2D objects: FILM
![Page 7: J-ICE – Tutorial: Build up a CRYSTAL - 1j-ice.sourceforge.net/oldwebpage/docs/01-Build-CRYSTAL.pdf · 2011-05-22 · J-ICE – Tutorial: Build up a CRYSTAL - 2 Click on the checkBox](https://reader033.vdocuments.mx/reader033/viewer/2022043016/5f38ecacc05edb773d0a1923/html5/thumbnails/7.jpg)
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