How To Install packmol on Fedora 34
Introduction
In this tutorial we learn how to install packmol on Fedora 34.
What is packmol
Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations. The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers. The user must provide only the coordinates of one molecule of each type, the number of molecules of each type and the spatial constraints that each type of molecule must satisfy. The package is compatible with input files of PDB, TINKER, XYZ and MOLDY formats.
We can use yum or dnf to install packmol on Fedora 34. In this tutorial we discuss both methods but you only need to choose one of method to install packmol.
Install packmol 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 packmol using dnf by running the following command:
sudo dnf -y install packmol
Install packmol 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 packmol using yum by running the following command:
sudo yum -y install packmol
How To Uninstall packmol on Fedora 34
To uninstall only the packmol package we can use the following command:
sudo dnf remove packmol
packmol Package Contents on Fedora 34
/usr/bin/packmol
/usr/bin/packmol_solvate
/usr/lib/.build-id
/usr/lib/.build-id/4b
/usr/lib/.build-id/4b/b3bbef758982d5512b449db9280c9bfeee95a0
/usr/share/doc/packmol
/usr/share/doc/packmol/AUTHORS
/usr/share/licenses/packmol
/usr/share/licenses/packmol/LICENSE
References
Summary
In this tutorial we learn how to install packmol on Fedora 34 using yum and dnf.