Hi everyone
I start learning RASPA recently by the manual and examples in the RASPA, but I get confused about the definition of radii in the pseudo_atom.def file. In the examples in RASPA, for CO2, C_co2 is 0.72 and O_co2 is 0.68. For tip5p water, Ow is 0.5 and Hw is 1.0. I cannot understand why those values are set. If the unit of radii is Angstrom? In the community forum, Dr. Dubbeldam explained that it is relative position of all atoms, but I still cannot understand it. Could you possibly give more detailed explanation about how to define radii in the pseudo_atom.def? For small rigid molecules, Could I not give the radii or just set all them to 1.0. Your help is appreciated.
These radii are only needed for flexible frameworks, and used as bond-criteria to determine bonding.
For other cases these values do not matter.
Dr. Dubbeldam, thanks for your answering.