How To Install packmol on Ubuntu 22.04
Introduction
In this tutorial we learn how to install packmol on Ubuntu 22.04.
What is packmol
packmol is:
Initial configurations for Molecular Dynamics Simulations by packing optimization.
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.
See http://m3g.iqm.unicamp.br/packmol for more information.
References
Please always cite one of the following references in publications for which Packmol was useful:
L Martinez, R Andrade, EG Birgin, JM Martinez, Packmol: A package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry, 30, 2157-2164, 2009. (http://www3.interscience.wiley.com/journal/122210103/abstract)
JM Martinez, L Martinez, Packing optimization for the automated generation of complex system’s initial configurations for molecular dynamics and docking. Journal of Computational Chemistry, 24, 819-825, 2003. (http://www3.interscience.wiley.com/journal/104086246/abstract)
There are three methods to install packmol on Ubuntu 22.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install packmol Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install packmol using apt-get by running the following command:
sudo apt-get -y install packmol
Install packmol Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install packmol using apt by running the following command:
sudo apt -y install packmol
Install packmol Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install packmol using aptitude by running the following command:
sudo aptitude -y install packmol
How To Uninstall packmol on Ubuntu 22.04
To uninstall only the packmol package we can use the following command:
sudo apt-get remove packmol
Uninstall packmol And Its Dependencies
To uninstall packmol and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:
sudo apt-get -y autoremove packmol
Remove packmol Configurations and Data
To remove packmol configuration and data from Ubuntu 22.04 we can use the following command:
sudo apt-get -y purge packmol
Remove packmol configuration, data, and all of its dependencies
We can use the following command to remove packmol configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge packmol
References
Summary
In this tutorial we learn how to install packmol package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.
