Getting Started

What is SAMSON?#

SAMSON is a software platform for computational nanoscience. Its generic, open architecture makes it suitable for life science, material science, physics, electronics, chemistry, and education. SAMSON stands for "Software for Adaptive Modeling and Simulation Of Nanosystems". The SAMSON application and the SAMSON SDK are developed by the OneAngstrom led by Stephane Redon.

Simulation of 1PV7 in SAMSON

SAMSON 2024 webinar recording#

To learn more about the recent SAMSON 2024 features please check out the webinar recording:

Here are the direct links to the different sections of the video:

00:00 OneAngstrom and SAMSON
03:16 SAMSON's top six distinctive features
06:55 Documentation and interactive tutorials
09:00 Getting answers and getting things done with SAMSON AI
13:15 Selecting with the Document View and the Context Toolbar
16:29 Selecting with the Viewport and Selection filters
17:37 Selecting with Selection Commands
18:35 Selecting with the Node Specification Language and SAMSON AI
21:26 Selecting with the new Interactive Sequence Viewer
23:47 Producing studio-quality renderings with Cycles, the integrated path tracer from Blender
26:32 Creating new visualizations quickly with the new Visual Preset Editor
31:52 Creating movies with the Animator
33:39 Using the new Cloud Job Manager and predicting protein structures
36:40 Importing and visualization GROMACS simulations
39:39 Creating apps and executable documents with the integrated Python Environment
43:17 Publishing documents securely and privately on SAMSON Connect
45:48 Creating and publishing your social profile on SAMSON Connect
46:26 Creating groups and organizing teams on SAMSON Connect
47:20 Sharing documents with users and groups
50:00 Beginning Q&A
51:10 Using Martinize to create coarse-grained structures
55:35 Importing and sharing cloud jobs
58:07 Contacting the developers

Current version#

The current version of SAMSON is 2024 R1.

Please refer to Versioning for more information about version numbers.

Supported platforms#

This version of SAMSON is supported on the following platforms:

Windows 11, Windows 10.
Linux: Ubuntu 22.04 and newer, CentOS, and other similar Linux OS.
macOS (64-bit Intel and ARM): Sequoia (macOS 15), Sonoma (macOS 14), Ventura (macOS 13), Monterey (macOS 12), Big Sur (macOS 11).

This version of SAMSON has not been tested on older OS platforms and might not be supported on them.

Requirements#

For running SAMSON, a 64-bit operating system and a graphics card supporting OpenGL 4.1 are required. For NVIDIA and AMD graphics cards an appropriate driver with an OpenGL support should be installed.

If you experience problems with OpenGL libraries, please check the Installing OpenGL drivers on Linux section.

Requirements on Linux:

On Ubuntu-like Linux, you might first need to install the libxcb-cursor0 library:

sudo apt install libxcb-cursor0

On CentOS-like Linux, you might first need to install xcb-util* packages:

sudo dnf install xcb-util*

What are SAMSON Extensions?#

SAMSON has an open architecture which allows you to extend it, and adapt it to your needs, by downloading SAMSON Extensions (modules) from the SAMSON Connect website. SAMSON Extensions come in many flavors: apps, editors, controllers, models, parsers, etc., and are adapted to different application domains. They help users build new models, perform calculations, run interactive or offline simulations, visualize and interpret results, and more.

Installing SAMSON#

Please, check the Requirements first.

To install SAMSON, download the SAMSON installer from this page on SAMSON Connect. You will be asked to sign in, or create an account if you don't have one. When you download the installer, a key will be sent to the email address you used for registration. You can also access your keys in your account on SAMSON Connect.

If you want to install an older version of SAMSON, please check How to install an older version of SAMSON.

Note

SAMSON Extensions are updated only for the latest version of SAMSON.

Start the SAMSON installer you just downloaded.

Note

On Linux, open a terminal in the folder where you downloaded the SAMSON installer and execute the following commands (make the installer executable and launch it):

chmod +x ./SAMSON-Setup.run
./SAMSON-Setup.run

Once the installer has started, you should see the following window:

The SAMSON installer

Note

Intel graphics cards may currently cause issues. If you have one, the SAMSON installer will generate a warning. You may choose to ignore the warning, especially if you also have a non-Intel graphics card (NVIDIA or AMD).

After accepting the license agreement, you reach a page that allows you to configure a proxy, if necessary:

Enter proxy parameters if necessary

At this point, the SAMSON installer checks that it can reach SAMSON Connect - the installer needs to download SAMSON and SAMSON Extensions. If it can, this page shows the message "SAMSON Connect reached successfully". Else, you might have to enter proxy parameters (you may have to ask your system administrator for information). Use the "Test connection" button to check that the proxy parameters you entered are valid.

Next, the installer asks you to enter the email address you used to register on SAMSON Connect, and the SAMSON key that was sent to you at that address when you downloaded the installer (you can also access your keys in your account on SAMSON Connect).

Enter your email address and the SAMSON key you received at that address

If you want, you may check the "Advanced mode" box to choose a custom installation path and specify which version of SAMSON you want to install (by default, the latest version is installed).

Then, the installer downloads SAMSON from SAMSON Connect, and installs it:

SAMSON is being downloaded from SAMSON Connect

Finally, the last page of the installer gives you the possibility to start SAMSON and visit SAMSON Connect:

SAMSON has been installed successfully

Post-installation steps on Linux:

To run SAMSON, you might need to install some xcb libraries.

On Ubuntu-like Linux, you might first need to install the libxcb-cursor0 library:

sudo apt install libxcb-cursor0

On CentOS-like Linux, you might first need to install xcb-util* packages:

sudo dnf install xcb-util*

Post-installation steps on macOS:

It might be necessary to provide a full disk access on macOS for SAMSON. Please see Full Disk Access In MacOS.

Starting SAMSON#

Here is how you start SAMSON depending on your operating system.

Windows#

On Windows, start SAMSON from the Start menu. Typing SAMSON in the search box might just lead you there. Else, SAMSON may be found in the SAMSON 6.0.0 folder:

C:\Users\USERNAME\OneAngstrom\SAMSON-Application\6.0.0\Binaries\SAMSON-Core.exe

Mac#

On Mac, start SAMSON from the launchpad or from the Application folder. The most recently SAMSON version will be launched.

SAMSON is installed in the following folder:

/home/Users/USERNAME/Applications/SAMSON-App/

Linux#

SAMSON installs a convenience shortcut file on the Desktop.

On Linux, open a terminal, go to your Desktop folder and execute:

./SAMSON_6.0.0

This is a link to the launching SAMSON-Core.sh script in the SAMSON installation folder. You might need to make this file executable:

chmod +x ~/Desktop/SAMSON_6.0.0

You can also directly launch the SAMSON-Core.sh script from the SAMSON installation folder path (it should be ~/OneAngstrom/SAMSON-Application/6.0.0/Binaries):

./SAMSON-Core.sh

You may create an alias in your '~/.bashrc':

alias samson='$HOME/OneAngstrom/SAMSON-Application/6.0.0/Binaries/SAMSON-Core.sh'

Now, open a new terminal and execute 'samson'.

In case you have issues on Linux with AMD/ATI graphics cards, please refer to the Troubleshooting section.

Extending SAMSON#

The first time you start SAMSON, it downloads a set of default SAMSON Extensions from SAMSON Connect. To customize your SAMSON installation from SAMSON Connect, simply sign in to your account, then go to the Marketplace to choose the SAMSON Extensions you need. Please refer to this page for more information.