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Like you say, if simulation-time was not an issue, then starting from a previous point helps with equilibration. But the computational cost is large, especially for higher pressures. So by submitting them all in parallel, you can compute the full isotherm at the costs of the time of the largest loading. For sequential running, you will need to wait for the result of the previous pressure. So, especially for isotherm with say 10-20 points, running them in parallel really helps.

You can use:
./run

Probably best to ask the creators of zeo++.

You are correct (and the manual has an error). You can put a list of pressures in the input, but only one temperature.
In practice, using a list of pressures is a bad idea, unless you really want to compute adsorption+desorption and examine hysteresis. The downside is that all simulations have to be run sequentially.

In practice, people develop scripts to submit batch-scripts to submit large number of jobs (for example: for various MOFs, various temperatures, various molecules, compute the isotherm over a pressure range).

An an inspiration, see the example scrips in the 'scripts' directory of the RASPA source.
You fill in the top-part, run the script and it will generate the input-files. A second script will read the data out of the output-files and put in a more useful format that can be used for plotting.

FIXED_BOND is for fixing a single bond, while the full molecule can still be flexible via bend and torsion potentials. An example is the TraPPE model for united-atom alkanes. In Monte Carlo it is easy to fix bonds because the bonds are _generated_. In Molecular Dynamics algorithms like shake needs to be used.
I would say that is better not to use fixed bonds, but rather use a harmonic bond-potential.

I would think they should be identical "in principle", if the force field (i.e. bond, bend, torsion parameters) is the same for both. So the molecule has the same type of atoms, same structure except R vs S.
Like you say, in practice they differ slightly, but the difference should vanish in the limit of running extremely long.

Your molecule has not diffused at all. I would first do a test with a small molecule so that you see what a graph looks like for a molecule that diffuses.
The y-axis is the MSD, in Angstrom squared. You can get diffusion results when the molecules diffuse at least through the repeating unit (so unit-cell-width squared).
In this case, MD is probably not capable of computing diffusion because it is too slow in your system.

See the many articles of Martin and Siepmann on this topic.

To compute pressure:
ComputeMolecularPressure yes

You can use a tool like "openbabel" to convert between different file formats.

See the examples for molecules. RIGID_BOND is used for molecules that are fully rigid, for example water or CO2. The bonding information is used for the CBMC-biasing.
RIGID_BOND is a type of bond-potential that has only one bond-distance.

MIL-101 is very large indeed. RASPA is not optimized for speed.  You can use a debugger to see where it goes wrong.

9% at those high pressure is still very, very good I would say. The validity of such a simple methane model is not "endless". Any classical model will show weaknesses at extreme conditions. Perhaps a full-atom model might do better, but these are harder to paremeterize.

1) As many cycles and molecules as you need. The more the better, but the slower the simulations. That's always a trade-off.
In equilibrium, the macroscopic properties no longer change. The amount of cycles needed to reach equilibrium depends on the system.
To limit finite size effects you need a large system. In practice you can simulate various system sizes as see when your properties converge to a plateau value as a function of system size.

2) in a NVT or muVT or Gibbs NVT simulation the energy fluctuates. This energy fluctuation is related to a physical property called the heat capacity.

3) There are no rules of thumbs, but rather it will take experience to get a feel for this.

Yes, all Qeq are differently implemented. The code in RASPA is based on the method of Wilmer and Snurr.
https://pubs.acs.org/doi/10.1021/jz3008485

The 'pseudo_atoms.def' contains predefined atoms, and this is often the way to go for molecules.
This especially important for united atom types etc.

For frameworks, read from a CIF file, there is always an element defined (_atom_site_type_symbol), and the type (_atom_site_label) is automatically added when found. The mass is a lookup from a database in 'src/scattering_factors.c'.