Open and manipulate bigger molecules

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Now that you know how to create your own molecules, you have to know how to save them and reopen them.

Open a “.pdb” file

Click on “File” then “Open…” or just press “Ctrl+O”, then select “chassis.pdb”. After you have clicked, a window should appear. Tick the boxes as done in this image:

figure1: Opening option window

Now open the file  “roue.pdb” four times.

Moving bigger molecules

On the display window you only see one molecule… But still, you opened it four times? Well, as you see in the document view, there are indeed four “roue.pdb”, they are just piled together. And you see that when you want to click on the molecule to move it, only an atom is moving.

To move the entire molecule, you have to select it in the document view. A yellow box should appear, meaning a group of atoms is selected, and now you can move it as one with  . Three arrows should appear, one for each direction. If you click on one of these arrows and drag the molecule in the direction of this arrow, it will move straight. If you click on one of the little black squares it will move in the plan containing the square like this:

figure2: Wheels positioning

You can now move all of the wheels to where they belong in order to make a nano-car (you can still use to move the group of atoms after it was selected).

Now that the wheels are in the right place, there is still a problem, beacause they are not in the right direction! To solve this, click on and click on the circle in the plane that you are working in, but not the yellow one which rotates the molecule in any direction.

figure3: Rotating Wheels

Creating the Nano-car

Create the bonds between the chassis and the wheels and save it by clicking on “File” then “Save as” or just hit “Ctrl+S” on your keyboard. Now you can run a simulation with no fear of having your work destroyed.

Once you have done this your computer gets slow. You can adjust some parameters of the simulation in order to speed things up, like reducing the number of steps and increasing the time between steps.

figure4: Parameter simulation

Increase the step size to at least 0.2 fs!

figure5: CNRS nanocar

Now try to place a carbon near the nano-car and watch what happens…

 

Quick! Stop the simulation!!!  →

Just press “Ctrl+Z” and it will be fine… Right?

It doesn’t recreate the bonds?  !@#$ !

Oh but you are a smart one and you saved your work earlier! You can just reopen it! pfiouu…..

As you may have seen, pressing “Ctrl+Z” moves you back in the “History”, but since the creation of bonds in the molecules you opened doesn’t appear, moving back won’t recreate them except if you’ve placed them yourself. And you also noticed how placing a single atom jammed the whole simulation so the next time you want to add molecules or atoms to a simulation, press this button:  first to pause the simulation!

And don’t forget to click on:  so you don’t create any atoms by accident, because the atom creator  was still selected.

 

Conclusion

What you have just assembled is a nano-car made by the CNRS for a race between labs. If you want to know more about them or the race where this car took part, you can follow these links:

www.cemes.fr/course_nanovoitures

http://nanocar-race.cnrs.fr/equipes-fr.php

We’ve created the parts ourselves on SAMSON with this topological representation:

 

figure6: Topological formula

 

 

 

 

 

 

If you want to try, you can do it yourself!

 

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