==========
MDAPackmol
==========
.. |travis| image:: https://travis-ci.com/MDAnalysis/MDAPackmol.svg?branch=master
:target: https://travis-ci.com/MDAnalysis/MDAPackmol
.. |coveralls| image:: https://coveralls.io/repos/github/MDAnalysis/MDAPackmol/badge.svg?branch=master
:target: https://coveralls.io/github/MDAnalysis/MDAPackmol?
|travis| |coveralls|
-----
## Why this fork?
MDAPackmol-fmt is a fork of the original MDAPackmol code adapted to the FillMyTubes code.
## MDAPackmol
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.
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