Dear all,
The pseudo_atom radii for N_N2 and NCOM_N2 are 0.7 in the pseudo_atoms.def file. The model for N2 molecule is taken from Potoff and Siepmann as the charge values for N and NCOM match with the partial charges given to these sites of N2 molecule of Potoff and Siepmann. How is the pseudo atom radius of 0.7 defined? What is the basis for the same. The experimental bond length of N2 molecule is 1.1 A.
The reason I am asking this question is because I want to define the pseudo_atoms for two CO models developed by Calero et al (2012) and Piper et al (1984). For these models, I have the LJ parameters, charges and the distance of the sites from the COM of the molecule. What should be the basis to define the pseudo_atom radii for each site of these models?
Thanks,
Rajasi
The radii are used to compute bonding in flexible frameworks.
For small rigid molecules you define the relative positions of all atoms (including for example dummy atoms).
Dear Prof. :
I wonder how to calculate the radii when we simulate a flexible molecue or framework indeed.
Sincerely.
You can look these radii up in handbooks.