Box.add_mol¶

Box.add_mol(short, link, inp, num_atoms='gro', auto_dens=None, mass=None, section='both', area=[], box=[], kwargs_gmx={})¶

Add a molecule to the simulation box. A unique short name and a structure-file link have to be given.

Furthermore, the input is either a specific number of molecules or the input fill in order to continuously fill the simulation box with the specified molecule. This can be done automatically by defining the reference density to fill up to.

The number atoms can either be specified numerically or extracted, which currently only works for the GROMACS file-type.

Parameters:

shortstring: Molecule short name as given in the topology
linkstring: Molecule structure file link
inpinteger, string: Define number of molecules or fill for filling a pore or box
num_atomsinteger, string, optional: Number of atoms in the specified molecule or filetype for extraction
auto_densfloat, None, optional: Density in \(\frac{\text{kg}}{\text{m}^3}\)
massfloat, None, optional: molecular mass (\(\frac{\text{g}}{\text{mol}}\)) of the molecule to get an estimate of how many molecules you need to put in the box as the initial value for auto_dens.
sectionstring, “both”, optional: ‘Both’ the molecules in the pore and in the reservoir can be set. If you want the molecules only in the pore, choose ‘pore’. If you want them only in the reservoir, choose ‘res’. For a slit pore you can use wall to put the molecules as a layer on the SiO2 surface. Chose “box” for a box system.
arealist, [], optional: To set up a 2-phase box system without a pore, specify the areas of the section [a,b] where the molecules should be inserted using Gromacs.
boxlist, [], optional: To set up a 2-phase system, specify the dimensions [x, y, z] of the simulation box.
kwargs_gmxdictonary, {}, optional: dictonary to set up options for the gromacs “insert-molecules” command (adjust for example -try and -scale)