This repository provides a python script to generate random molecular configurations taking into account periodic boundary conditions (pbcs) for large molecules. It supports partial pbcs, e.g. just in X and Y directions, which is realy useful for simulations with interfaces. Packmol software is required for running this tool so make sure you have it installed and cite it if you use this script.
The packing process starts putting one of the large molecules in an empty box. Then the molecule is randomly displaced which may lead in a configuration with part of the molecule outside the box so periodic boundary conditions are applied to bring back the atoms to the simulation box. After that, a new large molecule is put into that box. All these steps are repeated until a simulation box with all the large molecules is obtained. Finally, additional solvent molecules are packed inside that box if it is required.
As it was mentioned, Packmol is required as well as python 3.6 or grater and also the numpy and MDAnalysis python packages.
A basic usage of this tool would be to run in a terminal:
python pbc-packing.py input_info.json out_dir_name
The first argument (input_info.json) is the path to the file with all the
necessary information to perform the packing and the second one is a
directory which will be created to store all the outputs. The last is
optional and by default it will be set to packing. To write the
inpunt_info.json file see the structure of the
example that can be found in this repository. In the
next lines the meaning of each line in this example is commented:
{
// Specify the path to the packmol executable, this is, the
// command that you use to run packmol
"packmol_executable": "packmol",
// "pbc" is a list with three 0 or 1 refering to apply pbc in the (x, y, z)
// direction respectively. If the value is 1, pbcs are applied, else they
// are not. Its optional, by default pbcs are applied in the thre directions.
"pbc": [1, 1, 0],
// "box" is a list of floats corresponding to the dimension of the box in
// the x, y and z directions. If the list has just one value a cubic box
// will be created.
"box": [60],
// "large_molecules" is a dictionary specifying all the kind of large
// molecules that you want to put into the simulation box using pbcs.
"large_molecules": {
// For each kind of molecule you have to specify a name (PEO in this
// example).
"PEO": {
// If "replace" is false the large molecules that will be put into
// the box will be selected from the "paths" list without repetition
// otherwise, if it is true the same molecule can be randomly
// selected multiple times.
"replace": true,
// "amount" is the number of large molecule of this kind that you
// want to put into the box.
"amount": 20,
// "paths" is a list with all the available molecular configurations
// of this kind of large molecule that can be randomly selected to
// put into the box. NOTE: It is highly recomended to write absolute
// paths to the files. Also note that if "replace" is false "paths"
// must have at least "amount" different elements. If you only have
// one molecular configuration of this kind of large molecule you
// can set "replace" to true and just specify one path in "paths".
"paths": [
"../molecules/large/peo_0.pdb",
"../molecules/large/peo_1.pdb",
"../molecules/large/peo_2.pdb",
"../molecules/large/peo_3.pdb",
"../molecules/large/peo_4.pdb",
"../molecules/large/peo_5.pdb",
"../molecules/large/peo_6.pdb",
"../molecules/large/peo_7.pdb",
"../molecules/large/peo_8.pdb",
"../molecules/large/peo_9.pdb",
"../molecules/large/peo_10.pdb",
"../molecules/large/peo_11.pdb",
"../molecules/large/peo_12.pdb",
"../molecules/large/peo_13.pdb",
"../molecules/large/peo_14.pdb",
"../molecules/large/peo_15.pdb",
"../molecules/large/peo_16.pdb",
"../molecules/large/peo_17.pdb",
"../molecules/large/peo_18.pdb",
"../molecules/large/peo_19.pdb"
]
}
},
// At the end of the large molecule packing process you can optionally
// solvate the obtained box with other molecules which should be specified
// in the "solvent" section. Note all this solvent molecules will be put in
// the box at the same time without any kind of additional displacement.
"solvent": {
// For each solvent molecule specify the path to the pdb file with the
// molecular configuration and the amount of them you want in to be in
// the box. Again, we recomend to use absolute paths.
"../molecules/ace.pdb": 200,
"../molecules/ea.pdb": 200
}
}The script simply initializes an instance of the PBCPacking class with the
input parameters and then call its run_packing method. This class is also
documented so if you have any doubt do not hesitate to check it out.
In the current version, this tool only allows to generate orthoedric simulation boxes. On the other hand, although a box without solvent molecules can be generated at least one large molecule is required.