Messages

Just checked the code: the Widom move _does_ check for blocking.
How did you define the blocking-pockets and what is your input-file to switch on blocking for that component?

This workshop/school focuses on a practical understanding of visualization and molecular simulation of nanoporous materials and fluids, using iRASPA and RASPA. RASPA is well known for force field-based molecular simulation of adsorption and diffusion in nanoporous materials (such as MOFs and zeolites), as well as studying thermodynamic and transport properties of complex fluids. The combination with the visualization software iRASPA enables obtaining direct molecular insight. In this 1-day workshop, besides lectures on the basics of MD/MC, we will also consider the practical side of simulations using iRASPA/RASPA: setting up the system, constructing input files for molecules and frameworks, setting up a force field, understanding input settings, and analyzing the output. The workshop will be online.

https://iraspa.org/workshops/iraspa-raspa-online-workshop-2022/

The grids are tested by random insertion. So there is no mechanism that avoids overlap of the ions.
You can get: large negative Coulombic energy + large repulsive energy, that nearly cancels out.
So, this is more a problem of the test then of the grid itself.
You can run a simulation with and without the grid and see if you get the same answers.

You should not install it on /lib, which is indeed a read-only systems directory.
Better just install it in your home account.

In the raspa-directory do:
rm -rf autom4te.cache 
mkdir m4 
aclocal 
autoreconf -i 
automake --add-missing 
autoconf 
./scripts/CompileScript/make-gcc-local
make
make install

Probably best to ask the creators of zeo++.
Use a structure that you know is porous so you can interpret the values that zeo++ gives.

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.