========== MDAPackmol

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|travis| |coveralls|

An MDAnalysis_ wrapper around Packmol_

• Allows combining MDAnalysis and Packmol

• Preserves the topology information (bonds etc) of your system after Packmol

• Free software: GNU General Public License v3

.. _MDAnalysis: https://www.mdanalysis.org .. _Packmol: http://m3g.iqm.unicamp.br/packmol/home.shtml

Usage Example

.. code-block:: python

import MDAnalysis as mda import mdapackmol

load individual molecule files

water = mda.Universe('water.pdb') urea = mda.Universe('urea.pdb')

call Packmol with MDAnalysis objects as arguments

the 'instructions' allow for any valid Packmol commands

system = mdapackmol.packmol( [mdapackmol.PackmolStructure( water, number=1000, instructions=['inside box 0. 0. 0. 40. 40. 40.']), mdapackmol.PackmolStructure( urea, number=400, instructions=['inside box 0. 0. 0. 40. 40. 40.'])] )

the returned system is a MDAnalysis Universe

with all topology information from building blocks retained

which can then be saved into any format

eg to Lammps data file:

system.atoms.write('topology.data')

Citing

If you find mdapackmol useful for you, please cite the following sources:

• L Martinez, R Andrade, E G Birgin, J M Martinez, "Packmol: A package for building initial configurations for molecular dynamics simulations". Journal of Computational Chemistry, 30, 2157-2164, 2009.

• R J Gowers, M Linke, J Barnoud, T J E Reddy, M N Melo, S L Seyler, D L Dotson, J Domanski, S Buchoux, I M Kenney, and O Beckstein. "MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations." In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 102-109, Austin, TX, 2016.