First steps on SAMSON

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In this tutorial you will learn how to use SAMSON, or at least, after reading this, you should be able to know some of the basics of the software (like creating molecules, running simulations, etc..).

If you want more (maybe deeper) information regarding SAMSON, especially on its interface,  you can check out this link.

That is your survival guide on SAMSON if you encounter any troubles with the interface or a particular icon.

Opening up SAMSON

When you open SAMSON for the first time, you will see a window like this:

figure1: SAMSON interface

(1) : Menu

(2) : Toolbars

(3) : View window

(4) : Document view (everything you have created will appear and be sorted in “groups”)

(5) : Inspector (advanced configuration window for atoms, bonds, etc…)

(6) : History (every step you have done will be stored)

 

Before starting

Feel free to arrange the tool bar as you wish. Watch the gif below:

figure2: Interface handling

First atom

Click on “Atom creator”  found in “the toolbars (2)”.

If the icon is not found there, just press “A” – that is its shortcut. If you happen to create any atom by mistake and you want to delete them, you just need to select the tool “Point Selection” , then to click on an atom (press down “Ctrl” for multiple selections) and then press “Del”.

 

Now, click on the “view window (3)”. You should see a grey sphere on your screen…

It is nothing but a carbon atom.

By the way, if you look at your “Document view (4)” and your  “History (5)” windows, you should see something like this:

figure3: First atom

 

 

Your recently created carbon atom has been added into the list.

Note that, if it is in you history, it’s to allow you to “undo” what you have done before by clicking on an action. Try it for yourself if you want. For example: if you click on “New document” everything you have done should disappear (even in the history and document view) as soon as you perform a new action.

 

Other atoms

Click on the “Periodic table” , to access all the other atoms.

A window like this one should appear:

figure4: Periodic table

Click on the “Hydrogen” element and close the table window.

The periodic table icon should look like this:  (the little white square around it means that it is selected).

Click on the “view window (3)”.

An hydrogen atom should have joined your carbon atom on the screen, in the “Document View (4)” as well as in the “History (5)”.

figure5: Second atom

 

 

First bonds

Now, hold down “Left-Click” on one of your two atoms and move your cursor onto the other one.

figure6: First bonds

Conggratulations! You have just made your first atomic bond!

In a similar manner as for the two atoms, this bond should have been added to the “Document view (4)” and the “History”(5)”.

By clicking on “+”you can visualize what’s composing the bond (i.e your two carbon and hydrogen atoms).

figure7: History and inspector utilisation

 

 

Repeat this step three times, with three more hydrogen atoms.

 

To increase your accuracy, you can zoom in by holding down Shift+Mouse Wheel”.

Furthermore, you can change the viewing angle with the buttons   present on your toolbar, or just by pressing “Shift+Left-click”.

figure8: Moving around moleculs

By now, you should have noticed that your molecule is planar. Hopefully, you have also realized that you have created a methane molecule (chemical formula: C-H4).

Well… saying “created” is not quite right…

As you might know, methane is not a planar molecule, but with some “adjustments”, your methane will be looking just like the ones you are familiar with.

In order to do that, you will need to run a simulation…

But first, let’s take some time discussing this thing called SIMULATION.

The simulation

1) What is it good for ?

  • In physics, because that’s what these tutorials are all about, you probably know that a theory or a model is based on a system of equations.
  • In mechanics for example, you can have a model defined by its system of equations (let’s take Newton’s mechanical modeling as an example). If you do everything correctly, you just need to know :

-The system you are studying i.e. what you are going to put into your model

and

-What’s called the initials conditions.

 

  • With this, the result you are going to obtain will predict what the system will look like in the future…

…However, we have a lot of models with many beautiful equations, but…

  • In reality, it’s not always possible to find solutions (analytically) to these equations. Even if it was possible, sometimes there are hundreds and thousands of parameters meaning it’s completely impossible for any human to end up with a numerical result.

So how can we overcome this issue ? Because what we want is a result in order to compare it to the experiences we will make later.

 

  • In fact, with some ingenious computing methods and with one or more computers in which we introduce programs containing the equations and everything that constitutes the physical model, we end up with a simulation software, just like SAMSON.

 

So, now you might have a better understanding of what’s important to take into account beforehand, if you want to run a simulation.

The computing methods of the simulator

  • These will mostly influence the results you obtain after running the simulation. So you better know their limits, how they work and on which model(s) they rely on.
  • Because yes, in most cases, the simulation WILL give you a result, but it doesn’t mean that the result is correct or coherent…
  • That’s why it is extremely important (always and every time) to ask yourself the follwing questions when you are faced with some results, regardless of from where they come:

-What do I want to compute?

-What can I compute with this tool?

-What are the results I’m expecting from this? Or, at least, are the results correct in regards to what I know ?

 

2) Into the process of computation

In the end, all the computation parts are done by your computer and despite its power and its speed, if you give it a continuous function like you are used to manipulate in math, it will break it into discrete points.

But what’s the size from one point to another? And how many points am I going to end up with?

Let’s do an example (do it while you’re reading the text)

Draw the curve of a function on a piece of paper, you add an x-axis being the time scale along with an y-axis corresponding to the unit you need. And let’s say that your function starts at 0 second and ends at 100 seconds.

Now you have your best friend on the phone, and you want to tell him about the curve you just drew, but you can’t send him or her a picture of it…

How would you do to give your friend this curve in the “most” precise way? You want to make sure that he/she has almost the same thing drawn on his/her piece of paper, and if possible the exact same curve with a very small error.

Since you can’t tell your friend to “start on the left corner of your sheet then go upward, but just a bit and then move to the right a little…” we need to find another way.

 

Tell the friend to draw the x-axis just like you did. Now you could say “on the point ‘0 seconds’ on your x-axis, put the y-value 5 [units]. Then put at ‘100 seconds’ the y-value 10 [units]”. But with so little information, you won’t be sure the curve is drawn in the same way as you did… In order to do this, it is, in fact, quite a simple way… You just need to give your friend more points. Actually, the more points, the more similar curves.

So, in order to select these points, you can draw a mark on your x-axis every 1, 0.1, 10 seconds… or however precise you wish to be.

This is called the step size. If you choose a step size of 10 seconds, you’ll need to draw 9 marks (the one at ‘0’ and ‘100’ are already drawn). This is called the number of steps.

So the next thing you can tell the friend is to “divide your x-axis into different parts with a step size of 0.1 seconds”.

Now you just need to give him or her the y-value of 1000 points. Since this process of you giving the coordinates of a point and your friend noting them on his or her sheet takes one second for each point, it is going to take a while for all the points to be written down. Every one second, a point is placed by your friend, meaning that it will take you 1000 seconds (16 minutes and 40 seconds) to put all the points down on paper… This time is refered to as the execution process time.

You can say that you and your friend work with a processing frequency of 1Hz (one operation per second). For a simulation, this frequency corresponds to your processor frequency (for example, 3 GHz  means that it can perform three billion elementary operations in only one second). In your case, you have performed your simulation between 0 and 100 seconds, so it lasted for 100 second. This duration time is called the simulation time duration, which is completely different from the execution process time.    

 

So, the smaller your step size is, the “smoother” the simulation will be, and the more alike your and your friend’s curves will look. But it will of course take more time, since the number of steps has increased.

 

Let’s simulate!

After all these explanations on what a simulation is used for and why its useful, let’s finally run one ourselves…

 

Go to the “Simulation” tab and click on “Add simulator”, or use the shortcut Ctrl+Shift+M”.

figure9: Launch simulation

 

A window like this one should appear:

figure10: Launch simulation

You can give name your simulation. This name will be taken into account in the “Document view (4)”.

Make sure you have selected “Universal Force Field” and “Interactive modeling” as the interaction model and state updater.

 

For now, don’t be too concerned about what everything is for used for. You will see in more detail what it means in the upcoming tutorials.

 

A little window like this should appear. Click on  “OK”.

Two more windows have been opened. For now, don’t bother what they are used for, but with the previous explanation about “simulations”, you should be able to grasp what they are used for…

figure11: Simulation parameters

Don’t change anything here, and you can close all the windows.

 

The one thing remaining is just for you to run the simulation. This is done by clicking on the button “play simulation”   , or by pressing the “space bar”.

figure12: Running simulation

You should now see the atoms moving.

There you have it, your CH4 molecule! You can turn the camera around to verify that its not planar anymore.

 

Finally, select the tool “Point Selection”   and hold down “Left-Click” on an atom to move it around and observe that the molecule doesn’t break apart.

 

Conclusion

With this basic knowledge, you should now be able to understand and do all the others activities you can find here, in which a physical principle or a SAMSON aspect will be explained in detail.

 

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