Messages

What do you mean with a "totally destroyed structure"? Are you using a flexible model? In that case you need a good force field to describe the flexibility of the framework.
For a rigid structure, the end and begin structure should of course be identical. In case you meant a rigid structure, then check whether the space-group is given correctly. You can always change your structure to a P1 structure, so that there are no space group issues.

See the manual for these options.

'ComputeMSDConventional'  for conventional MSD, and 'ComputeMSD' for order-n MSD (works in log-scale).

Correlation times are usually much smaller than total simulation time, because you need to average a lot to get good statistics. You could only have one measurement of a correlation time equal to your simulation length and that point would be useless.

If you use a flexible framework, then all atoms should move. In MD that is done automatically; in MC you need MC-moves to do that.

There is a new example added to the last version (v2.0.31): examples/Advanced/dcTST-LTA_SI.
See also the updated raspa.pdf in: Docs.

I am not sure, but you can always try it and sees if it works or not.

For all force field files, use your own values. All force field files in RASPA are just meant as examples.
The important value are epsilon and sigma for the Lennard-Jones.
The radii in the 'pseudo_atoms.def' are only used to compute bonds.

The files with 'self' are self-diffusion, the 'total' file is self-diffusion of the total fluid (so independent of the component type). So for a single component run the output for the component and the total is the same. For a multi-component mixture they differ. The files with 'onsager' in the name contain mixture Onsager coefficients.
Note the files contains in the columns:
1: correlation time in picoseconds.
2: MSD averaged over x,y,z (number of dimensions = 3).
3: MSD in the x-direction  (number of dimensions = 1).
4: MSD in the y-direction (number of dimensions = 1).
5: MSD in the z-direction (number of dimensions = 1).
6: number the times this point has been computed.

The source for this is `src/sample.c'.

No, you do that by setting for the component:
FugacityCoefficient 1.0
Then you compute vs fugacity (see the manual).

https://www.tudelft.nl/2018/3me/april/geavanceerde-gratis-app-iraspa-voor-moleculaire-visualisatie/

Yes, but you can look them up somewhere if you need them. These are used to convert pressure to fugacity using an equations of state.
Alternatively, if you use fugacity in your simulations (instead of pressure) then these number are not used.

What's new in this version:
• Greatly improved drag and drop, and copy and paste, for the project- and scene-panes (using concurrent background queues).
• Added and modified the 'New"-menu item under 'File'.
• Properly implemented the add- and remove-buttons for the project- and scene-panes.
• Many, many bug-fixes for crystal, molecular crystal, protein crystal, molecule, and protein.
• Updated for Swift 4.1.

For any error, always retry with the latest version (which is RASPA 2.0.30).

These structures are either from experiment (published in the literature) or from the IZA website.

If you want to minimize a zeolite or MOF structure, then you need a forcefield for it (and a good one).
So yes, options "FlexibleFramework and FrameworkDefinitions" need to be there and FrameworkDefinitions.def needs to contain a good force field for the framework.

If you want to minimize molecules inside the framework, the you can keep the framework fixed and "FlexibleFramework and FrameworkDefinitions" are not needed.

See the manual for the format of the file. If you add an interaction you need to increase the number of interactions.
Change
# number of defined interactions
28
to
# number of defined interactions
29

Macs in Chemistry:
https://www.macinchem.org/blog/files/27037cf7a65316151625e49f7f5c5cda-2283.php