How To Install smoldyn on Fedora 34
Introduction
In this tutorial we learn how to install smoldyn on Fedora 34.
What is smoldyn
Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of interest individually to capture natural stochasticity and to yield nanometer-scale spatial resolution. It treats other molecules implicitly, enabling it to simulate hundreds of thousands of molecules over several minutes of real time. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes much as they would in a real biological system. It is more accurate and faster than other particle-based simulators. Smoldyn unique features include manipulate or measure the simulated system, support for spatial compartments, molecules with excluded volume, and simulations in 1, 2, or 3 dimensions.
We can use yum or dnf to install smoldyn on Fedora 34. In this tutorial we discuss both methods but you only need to choose one of method to install smoldyn.
Install smoldyn on Fedora 34 Using dnf
Update yum database with dnf using the following command.
sudo dnf makecache --refresh
The output should look something like this:
Fedora 34 - x86_64 20 kB/s | 6.6 kB 00:00
Fedora 34 openh264 (From Cisco) - x86_64 1.4 kB/s | 989 B 00:00
Fedora Modular 34 - x86_64 68 kB/s | 6.5 kB 00:00
Fedora 34 - x86_64 - Updates 3.5 kB/s | 6.2 kB 00:01
Fedora Modular 34 - x86_64 - Updates 17 kB/s | 5.9 kB 00:00
Metadata cache created.
After updating yum database, We can install smoldyn using dnf by running the following command:
sudo dnf -y install smoldyn
Install smoldyn on Fedora 34 Using yum
Update yum database with yum using the following command.
sudo yum makecache --refresh
The output should look something like this:
Fedora 34 - x86_64 20 kB/s | 6.6 kB 00:00
Fedora 34 openh264 (From Cisco) - x86_64 1.4 kB/s | 989 B 00:00
Fedora Modular 34 - x86_64 68 kB/s | 6.5 kB 00:00
Fedora 34 - x86_64 - Updates 3.5 kB/s | 6.2 kB 00:01
Fedora Modular 34 - x86_64 - Updates 17 kB/s | 5.9 kB 00:00
Metadata cache created.
After updating yum database, We can install smoldyn using yum by running the following command:
sudo yum -y install smoldyn
How To Uninstall smoldyn on Fedora 34
To uninstall only the smoldyn package we can use the following command:
sudo dnf remove smoldyn
smoldyn Package Contents on Fedora 34
/usr/bin/smoldyn
/usr/lib/.build-id
/usr/lib/.build-id/21
/usr/lib/.build-id/21/cf3baf0c796a395b151af4f63f4fa980171f04
/usr/share/licenses/smoldyn
/usr/share/licenses/smoldyn/License.txt
/usr/share/licenses/smoldyn/SFMT-LICENSE.txt
References
Summary
In this tutorial we learn how to install smoldyn on Fedora 34 using yum and dnf.