Defining new molecules for RASPA MC Calculation

[manuelbenavent]

Dear user

I´ve been using RASPA over the course of a week now and I went through the most relevant examples. Right now I want to test RASPA in my research problem, studying the adsorption of simple amine molecule with ZSM-5 Al-containing zeolites. I´ve tried to prepare a pyridine.def input file (below) prepared from the benzene.def file (as an example) and using the cartesian position obtained from Avogadro. However, I´m not sure if this position are the relative position mentioned in the documentation of RASPA. Also I´ve inserted all the bonds by hand.

Please give me some feedback about this input file and also advice on tools that can make the preparation of such input easier.

Thanks
Manuel

INPUT
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
620.0
5630000.0
0.243
# Number Of Atoms
11
# Number of groups
1
# pyridine-group
rigid
# number of atoms
11
# atomic positions
0   H         -0.85810        2.22423        0.90914
1   C         -1.81118        2.67173        1.20875
2   N         -2.95932        1.88839        1.26755
3   C         -4.17052        2.45702        1.64822
4   H         -5.07401        1.84063        1.69441
5   C         -4.23369        3.80891        1.97015
6   H         -5.18679        4.25635        2.26970
7   C         -3.08557        4.59223        1.91130
8   H         -3.13530        5.65605        2.16450
9   C         -1.87436        4.02364        1.53064
10   H         -0.97089        4.63998        1.48433
# Chiral centers Bond  Bend  UrayBradley InvBend  Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Bend/Torsion IntraVDW IntraCoulomb
               0   11     0            0       0        0            0         0            0         0            0        0            0
Bond stretch: atom n1-n2, type, parameters
0 1 RIGID_BOND
1 2 RIGID_BOND
1 9 RIGID_BOND
2 3 RIGID_BOND
3 4 RIGID_BOND
3 5 RIGID_BOND
5 6 RIGID_BOND
5 7 RIGID_BOND
7 8 RIGID_BOND
7 9 RIGID_BOND
9 10 RIGID_BOND
# Number of config moves
0

[dubbelda]

The positions are relative to each other. In the output file you can see that it reorients the molecule anyway (according to the matrix of inertia).

[manuelbenavent]

The positions are relative to each other. In the output file you can see that it reorients the molecule anyway (according to the matrix of inertia).

Dear Dubbelda

But is this ok for me to define the pyridine´s atoms in such a way?

Allow me another question. I want to prepare an MFI zeolite structure in a 1x1x2 with a single Al atom and a corresponding H as counterion. What is the best way for me to prepare such input? I´ve tried to open an MFI.cif file, build a 1x1x2 supercell, and adding both the Al and the H in Avogadro. But it seems that the way is written by Avogadro is not compatible with RASPA. Can you also provide some insight into this?

Thanks
Manuel