mdapackmol's Introduction

MDAPackmol

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.

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