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Hi,

you have to look for the units in the RASPA2 manual. For example:

HARMONIC_BOND

describes bonds and needs two parameters with units K/A^2, A.

From the LigParGen server, you can get the topologies in different formats. I used the GROMACS itp file, the units used in GROMACS can be found here: https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html

So GROMACS uses units kJ/(mol*nm^2), nm. The conversion from nm to A is straightforward, but in the first case we need:
a) convert from kJ/mol to J (multiply by 1000 and divide by Avogadro's constant),
b) convert from nm^-2 to A^-2 (divide by 100),
c) convert from J/A^2 to K/A^2 (divide by Boltzmann's constant)

that brings us to multiply the value from GROMACS' itp file by 1.2037. In the same manner, you would obtain SIX_COSINE_DIHEDRAL potential in RASPA2 from GROMACS' RB dihedral parameters values by multiplying them by 120.272355. Please refer to the manual of RASPA2. And also please be aware that if you have no experience with such simulations, it can take a few days (or even weeks) to understand how to prepare inputs properly and run the simulations correctly.

Also, as you will be preparing the forcefield description, please pay attention to the Lennard-Jones parameters. You need to perform such a conversion as well. In some cases, like in the case of the Dreiding forcefield, you also need to check if the values are scaled in relation to the equation used in RASPA2. You need to read the manual and papers to understand everything correctly, and that can be challenging.

Cheers,
Mateusz

Hi,

the parameters that describe the torsion angles (as well as other parameters describing both the bonding and non-bonding interactions) are a part of a specific forcefield, in the example you provided, the TraPPE forcefield. You did not specify what molecule you are interested in. You can find the TraPPE forcefield description here: http://trappe.oit.umn.edu/. You can find there, for example, 2,3-dimethylbutane, which shares the dihedral parameters with 2-methylbutane.

Bear in mind, however, that description of a molecule within a forcefield is not an easy task. You can also try the OPLS-AA forcefield in a case you cannot find your molecule within the TraPPE, here is a generator of the parameters: http://zarbi.chem.yale.edu/ligpargen/

In either case please remember to make sure you use the proper units of the parameters in RASPA. It may be also a good thing if you read a bit about the forcefields in atomistic simulations.

Cheers,
Mateusz

Hi,

my experience with RASPA is not great, but it took me a few weeks to set my system up properly, so I can share with you some advice:

1) in the force_field_mixing_rules.def file you put the non-bonding interactions, which in your case probably means the Lennard-Jones epsilon and sigma values (yes, epsilon/kb as given the SI). Pay attention to the cut-off defined in the simulation.input as well as if there are tail corrections applied to the potential. In force_field.def you explicitly define interactions (meaning you'd have to define C-C, C-O, C-H, etc.). In most cases anyway, the forcefields utilize the mixing rules, so you do not have to do that. In that case, you leave the force_field.def "empty" (not literally empty, there is still some input that says there are no rules to overwrite. Just look at the example forcefields provided with RASPA).

2) in the pseudo_atoms.def file you define (in most cases) the atoms of your adsorbate. That means you define what atoms create your molecule by assigning appropriate chemical elements and masses to the atoms (as you can see in the provided files). The labels used in that file must correspond to the ones used in the molecule.def file later. As you want to study CO2/H2O adsorption, and the paper you linked is about alkanes, you have to find the parameters (both for LJ and charges) somewhere else. It can be TraPPE in the case of CO2, and you have plenty of water models to choose from. The charges should be provided there.

3) charges of the MOFs in the SI: the best option is to include them directly in the CIF file. Look at the CIFs distributed with RASPA, you just define a new field in the CIF and that's it. Of course, make sure you match atoms between your CIF file and the ones in the SI. Your CIF may have more atoms than in the SI: either your CIF does not describe the smallest asymmetric unit or/and your CIF describes different symmetry, hence the difference in the number of atoms. If you have used VASP for the geometry optimization, you can probably get the DDEC charges as well if there is a mismatch between their description of the MOF and yours. You can also use built-in charge equilibration method to get the charges, or use some machine learning-based charges (google for PACMOF, for example).

Again, I may be wrong as I still learn RASPA and MC in general. You will also have to spend a lot of hours learning how to use RASPA.

Cheers,
Mateusz