Mobile adsorbate method

[Jakob Brauer]

Dear all,

I am interested in computing the free energy of adsorption for pharmaceuticals in zeolites, following the paper https://doi.org/10.1021/ct1005505 .

From the examples distributed with tamkin I adapted the physisorption script, please find attached the script ppcp-adsorption.py .

I failed to reproduce the methodology presented in the paper https://doi.org/10.1021/ct1005505. By using the "mobile" option in the construction of the partition function for the molecule-zeolite structure, I understand that the translations of the adsorbed molecule are accounted for in the partition function and thus in the entropy and free energy. However, the vibrational modes that correspond to translations of the adsorbate are still evaluated as vibrations to my understanding, right?

The attached script find_rot-trans-frequencies.py determines which vibrational modes correspond to rotations or translations of the adsorbate. I don't understand how I can remove these vibrations from the hessian before contructing the partition function for the adsorbed structure and how to evaluate these rotations as such to end up with the mobile-adsorbate partition function as it is definded in the paper linked above.

Any help would be appreciated.

Kind regards and best wishes

Jakob

[tfjer...@gmail.com]

Dear Jakob,

I don't know if the following solves your problem, but setting dim=3 in the line below does not make sense to me. An adsorbate that can translate in three dimensions is not adsorbed (according to my understanding).

pf_both = PartFun(nma_both, [ExtTrans(cp=False, dim=3, mobile=FU_atoms)])

Best regards,

Torstein

[tfjer...@gmail.com]

Dear Jakob, 

I have now investigated the issue myself, and it seems like the suggestion I made yesterday is irrelevant. 

When I add translational degrees of freedom to the mobile adsorbate and print information about the partition function, it says that the number of vibrational frequencies is still the same as originally. 

It seems like the vibrational degree of freedom that corresponds to translation is not removed. I have not found out how one can remove the vibration manually. Maybe the developers can provide some explanation. 

Best regards,

Torstein