Make water box#

Generating a box of water molecules with specified dimensions.

The function molsysmt.build.make_water_box() fills a periodic box of specified dimensions with water molecules at standard density.

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.build.make_water_box().

Basic usage#

Let’s show how to create a rectangular water box using numpy box dimensions:

import molsysmt as msm
import numpy as np

We define a cubic box of length 2.0 nanometers:

box = np.array([[[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0]]]) * msm.pyunitwizard.unit('nm')

Now we pass the box dimensions to molsysmt.build.make_water_box() to generate the solvated box:

molsys = msm.build.make_water_box(box)

msm.info(molsys)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_waters	n_structures
molsysmt.MolSys	804	268	268	1	268	1	268	1

We can verify that the oxygen atom coordinates fall strictly within the box boundaries:

coordinates = msm.get(molsys, selection='atom_type=="O"', coordinates=True)

print(f'Min X: {coordinates[0,:,0].min()} and Max X: {coordinates[0,:,0].max()}')

Min X: 0.004029999999999978 nanometer and Max X: 1.99909 nanometer