How To Install packmol on Kali Linux

In this tutorial we learn how to install packmol on Kali Linux. packmol is Initial configurations for Molecular Dynamics Simulations

Introduction

In this tutorial we learn how to install packmol on Kali Linux.

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 Kali Linux. 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 on Kali Linux first since aptitude is usually not installed by default on Kali Linux. 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 Kali Linux

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 Kali Linux, we can use the command below:

sudo apt-get -y autoremove packmol

Remove packmol Configurations and Data

To remove packmol configuration and data from Kali Linux 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

Dependencies

packmol have the following dependencies:

References

Summary

In this tutorial we learn how to install packmol package on Kali Linux using different package management tools: apt, apt-get and aptitude.