Packmol - Creates Initial Configurations for Molecular Dynamics Simulations
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.
User guide, examples, and tutorials, are available at: https://m3g.github.io/packmol
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.
-
Download the
.tar.gz
or.zip
files of the latest version from: https://github.com/m3g/packmol/releases -
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.
-
Go into the
packmol
directory, and compile the package (we assumegfortran
or other compiler is available):cd packmol ./configure [optional: path to fortran compiler] make
-
An executable called
packmol
will be created in the main directory. Add that directory to your path.
-
Install the Fortran Package Manager from: https://fpm.fortran-lang.org/en/install/index.html#install
-
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 apackmol
command anywhere in your computer.fpm
will look for Fortran compilers automatically and will usegfortran
as default. To use another compiler modify the environment variableFPM_FC=compiler
, for example forifort
, use in bash,export FPM_FC=ifort
.
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)