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
Usage Example
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.