Messages

It would be inconsistent if the host-host contribution would be ignore. The large value is because you have a lot of VDW pairs in the framework.
Note: if a particle moves from A to B, in the energy difference that value cancels out. So it has little influence on adsorption, only via the positions of the framework atoms.

No, the bonds are not read, and dynamically recomputed. VMD can read the bonds from file I think (without recomputing them).

The number of molecules in Gibbs is an input parameter. Usually you want a sufficient number of molecules to reduce finite size effects (like 256 or 512) in liquid/vapor equilibrium Gibbs.
In case of adsorption, you need more molecules that the saturation loading in the framework plus then enough molecules in the vapor phase.

No, but you could achieve this with scripts. Just simulate at a certain temperature, and use the restart-file to restart at a lower temperature.

Note that force fields like 'GenericMOFs' are only examples (just like any molecule or structure file), just for the example cases in the code to work. For any real work you need to create and develop your own force fields, or take them from from the literature, and carefully construct, check and validate them.

Also, orthorhombic is much faster than triclinic. For triclinic structure, the distance computation is a matrix multiplication to get fractional coordinates, then apply periodic boundary conditions, and then convert back to Cartesian space.

It might be that if you choose the atomic positions wrong, that the molecules can overlap. This happened in particular with for example water where the larger oxygen shield the hydrogens. Often the hydrogens do not have a VDW parameter because the repulsion of the oxygen is sufficient. Choosing a wrong repulsion (too small sigma) leads to overlap with the hydrogens and hence numerical issues. So with classical force fields you should always be aware and avoid unphysical situations.

The reason for the warning is that using CBMC with regrow is not advisable when the molecule has a net charge. The energies could become why to small/large leading to under/overflow.
It is better than for cations to use 'random translation'.

If the net-charge changes it can be because the adsorbate has a (small) net charge. With inserting adsorbates it will then grow in magnitude.

Using the 'binary' file, the simulation should immediately end, since it was already finished. There is no wya to extend a binary restart.
The other form of restart just use the initial positions written as output from the previous run.
The positions are written to 'Restart', while reading is from 'RestartInitial' to avoid overwriting these.
To restart, copy 'Restart' to 'RestartInitial'.
If results are different, then you did not equilibrate long enough.

Check the manual and examples. There are explicit examples for mixtures and adsorption mixtures,
for example:
examples/Basic/MC_BinaryMixture_in_Box
examples/Non-Basic/Adsorption_of_Binary_mixture_CO2_CH4_in_IRMOF-1

[outside]

Do you mean that you want to simulate adsorption on the outside of the zeolite?
Because using the grand-canonical approach only the adsorbed phase inside the framework is computed.

I have no experience with adsorption on the external surface of a zeolite.

Did you set the 'IdealGasRosenbluthWeight'?

Since every flexible model changes the reference chemical potential, the IdealGasRosenbluthWeight needs to be explicitly computed using a simulation of a single molecule in an empty box, and then used as the reference in the adsorption simulation.

I re-ran "examples/Non-Basic/MC_Adsorption_of_CO2_in_LTA4A_Sodium" without problems.
There was however a small memory-issue which could affect this, so you could retry with version 2.0.40.

But usually "illegal instruction" is related to the compiler, for example compiling on intel-type A and then running on intel-type B.

Did you define a flexible-ring? (RASPA can not handle flexible rings).

See the example: Non-Basic/Adsorption_of_Binary_mixture_CO2_CH4_in_IRMOF-1
You specify total pressure and mol-fractions. Partial fugacities are computed and written to the output-file.


ExternalTemperature 300.0
ExternalPressure  10e5

Component 0 MoleculeName               CO2
            MolFraction                0.25

Component 1 MoleculeName               methane
            MolFraction                0.75