How To Install smoldyn on CentOS 8

smoldyn is A particle-based spatial stochastic simulator

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.