How To Install smoldyn on Fedora 36

In this tutorial we learn how to install smoldyn in Fedora 36. smoldyn is A particle-based spatial stochastic simulator

Introduction

In this tutorial we learn how to install smoldyn on Fedora 36.

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 36. In this tutorial we discuss both methods but you only need to choose one of method to install smoldyn.

Install smoldyn on Fedora 36 Using dnf

Update yum database with dnf using the following command.

sudo dnf makecache --refresh

After updating yum database, We can install smoldyn using dnf by running the following command:

sudo dnf -y install smoldyn

Install smoldyn on Fedora 36 Using yum

Update yum database with yum using the following command.

sudo yum makecache --refresh

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 36

To uninstall only the smoldyn package we can use the following command:

sudo dnf remove smoldyn

smoldyn Package Contents on Fedora 36

/usr/bin/smoldyn
/usr/lib/.build-id
/usr/lib/.build-id/a0
/usr/lib/.build-id/a0/ae48b398bcfcd3e100a4ef56b96e268e7b614f

References

Summary

In this tutorial we learn how to install smoldyn on Fedora 36 using yum and [dnf]((/fedora/36/dnf/).