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Make sure the box is large enough so that the molecules can be placed in the box without overlap.
If your chosen amount of molecules cannot be placed in the chosen box, then it hangs for ever.

Yes, it is a UFF/Dreiding combination, to just have a generic force field to use for the examples.
For any realistic simulations you would probably use your own chosen force field.

You can fit them in any way that you want, the models are just a description of the isotherm.
RUPTURA fits a single isotherm with a chosen model. For dual-site Langmuir you get 4 parameters back that give a functional form of the isotherm. You could also fit the isotherm with your own software and put in the obtained parameters in RUPTURA to then compute the breakthrough using that isotherm model and parameters.

Yes, rigid molecules are supported. Also, per component you can block or allow certain regions for insertion/deletion.

You have not specified the interactions for C-O C-Ca C-CH4_sp3 Ca-C Ca-O Ca-CH4_sp3 CH4_sp3-C CH4_sp3-O CH4_sp3-C CH4_sp3-O CH4_sp3-C CH4_sp3-O CH4_sp3-C CH4_sp3-C etc. Generally you will need to define these in the 'force_field_mixing_rules.def' file, using a self-interaction and a mixing rule to get the cross-interactions.

There are packages for linux, including centos 7 at:
https://github.com/iRASPA/RASPA3/releases

You probably used "surface"-rendering. With "volume-rendering" you can get more of a color-gradient.
Bonding is controlled by a general rule, also employed by VMD: The radius < (covalent radius of atom1 + atom2 + 0.56).

No, RASPA does not use parallelism. But, for example, usually each point in an isotherm is computed separately and you can use an "embarrassingly parallel" approach.

No, that is not possible. Usually docking software is used for that. I would look into 'gromacs' for biomolecules as a start.

In principle there is no limit. But Monte Carlo is limited to small molecules, usually molecules of 1-20 atoms. 30 atoms is already considered very, very large.

That is what makes classical simulations more difficult than quantum. But for many systems, forcefields have been published in the literature.

In RASPA2 you input the final result: the partition-factor. In more recent RASPA versions the Log of the partition function to avoid over/underflow.
It is an user input, and up to the user to compute it.

You can look these radii up in handbooks.

You could modify the RASPA code, or label the atoms differently.

I would modify the force field. One of the options is to put a hard-sphere potential around the hydrogen to shield it from overlap.