How To Install packmol on CentOS 8
Introduction
In this tutorial we learn how to install packmol on CentOS 8.
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 CentOS 8. In this tutorial we discuss both methods but you only need to choose one of method to install packmol.
Install packmol 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 packmol using dnf by running the following command:
sudo dnf -y install packmol
Install packmol 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 packmol using yum by running the following command:
sudo yum -y install packmol
How To Uninstall packmol on CentOS 8
To uninstall only the packmol package we can use the following command:
sudo dnf remove packmol
packmol Package Contents on CentOS 8
/usr/bin/packmol
/usr/bin/packmol_solvate
/usr/lib/.build-id
/usr/lib/.build-id/3e
/usr/lib/.build-id/3e/84133badf8eeb3005e4e52a36841c470a415bc
/usr/share/doc/packmol
/usr/share/doc/packmol/AUTHORS
/usr/share/doc/packmol/LICENSE
References
Summary
In this tutorial we learn how to install packmol on CentOS 8 using yum and dnf.