biocheming/packmol

Packmol - Initial configurations for molecular dynamics simulations

Packmol

Packmol - Creates Initial Configurations for Molecular Dynamics Simulations

This page contains the version history of Packmol. You can download packmol from this page, but give preference to the official Packmol page:

http://m3g.iqm.unicamp.br/packmol

Detailed installation and usage instructions are available at this home-page.

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.

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)