Packmol

Packmol - Creates Initial Configurations for Molecular Dynamics Simulations

https://m3g.github.io/packmol

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.

Usage

User guide, examples, and tutorials, are available at: https://m3g.github.io/packmol

Installation instructions

Multi-platform package provider with Julia

If you are not familiar with compiling packages, you may find it easier to get the Julia interface for packmol, which provides executables for all common platforms: https://github.com/m3g/Packmol.jl

Installation of the Julia programming language and of the Julia Packmol package are necessary, but these follow simple instructions which are described in the link above.

Compilation of the package, particularly on Linux platforms is, nevertheless, easy, following the instructions below.

Downloading

1. Download the .tar.gz or .zip files of the latest version from: https://github.com/m3g/packmol/releases

2. Unpack the files, for example with:

   tar -xzvf packmol-20.13.0.tar.gz

   or

   unzip -xzvf packmol-20.13.0.zip

   substituting the 20.13.0 with the correct version number.

Using make

3. Go into the packmol directory, and compile the package (we assume gfortran or other compiler is available):

   cd packmol
   ./configure [optional: path to fortran compiler]
   make

4. An executable called packmol will be created in the main directory. Add that directory to your path.

Using the Fortran Package Manager (fpm)

3. Install the Fortran Package Manager from: https://fpm.fortran-lang.org/en/install/index.html#install

4. Go into the packmol directory, and run:

   fpm install --profile release

   this will compile and send the executable somewhere in your PATH. By default (on Linux systems) it will be ~/.local/bin. Making it available as a packmol command anywhere in your computer.

   fpm will look for Fortran compilers automatically and will use gfortran as default. To use another compiler modify the environment variable FPM_FC=compiler, for example for ifort, use in bash, export FPM_FC=ifort.

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)