Introduction
In this tutorial we learn how to install smoldyn on CentOS 8.
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’s 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 CentOS 8. In this tutorial we discuss both methods but you only need to choose one of method to install smoldyn.
Install smoldyn on CentOS 8 Using dnf
Update yum database with dnf using the following command.
sudo dnf makecache --refresh
The output should look something like this:
CentOS Linux 8 - AppStream 43 kB/s | 4.3 kB 00:00
CentOS Linux 8 - BaseOS 65 kB/s | 3.9 kB 00:00
CentOS Linux 8 - ContinuousRelease 43 kB/s | 3.0 kB 00:00
CentOS Linux 8 - Extras 23 kB/s | 1.5 kB 00:00
CentOS Linux 8 - FastTrack 40 kB/s | 3.0 kB 00:00
CentOS Linux 8 - HighAvailability 36 kB/s | 3.9 kB 00:00
CentOS Linux 8 - Plus 24 kB/s | 1.5 kB 00:00
CentOS Linux 8 - PowerTools 50 kB/s | 4.3 kB 00:00
Extra Packages for Enterprise Linux Modular 8 - x86_64 13 kB/s | 9.2 kB 00:00
Extra Packages for Enterprise Linux 8 - x86_64 24 kB/s | 8.5 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 CentOS 8 Using yum
Update yum database with yum using the following command.
sudo yum makecache --refresh
The output should look something like this:
CentOS Linux 8 - AppStream 43 kB/s | 4.3 kB 00:00
CentOS Linux 8 - BaseOS 65 kB/s | 3.9 kB 00:00
CentOS Linux 8 - ContinuousRelease 43 kB/s | 3.0 kB 00:00
CentOS Linux 8 - Extras 23 kB/s | 1.5 kB 00:00
CentOS Linux 8 - FastTrack 40 kB/s | 3.0 kB 00:00
CentOS Linux 8 - HighAvailability 36 kB/s | 3.9 kB 00:00
CentOS Linux 8 - Plus 24 kB/s | 1.5 kB 00:00
CentOS Linux 8 - PowerTools 50 kB/s | 4.3 kB 00:00
Extra Packages for Enterprise Linux Modular 8 - x86_64 13 kB/s | 9.2 kB 00:00
Extra Packages for Enterprise Linux 8 - x86_64 24 kB/s | 8.5 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 CentOS 8
To uninstall only the smoldyn package we can use the following command:
sudo dnf remove smoldyn
smoldyn Package Contents on CentOS 8
/usr/bin/smoldyn
/usr/lib/.build-id
/usr/lib/.build-id/31
/usr/lib/.build-id/31/2c99bc0b4748a37970f62848f5c07f4cbf7995
/usr/share/doc/smoldyn
/usr/share/doc/smoldyn/SFMT-README.txt
/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 CentOS 8 using yum and dnf.
