Author Topic: How to define 'radii' in the pseudo_atom.def file  (Read 489 times)

j.pu@hotmail.com

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How to define 'radii' in the pseudo_atom.def file
« on: June 06, 2022, 02:51:23 PM »
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.

David Dubbeldam

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Re: How to define 'radii' in the pseudo_atom.def file
« Reply #1 on: June 09, 2022, 01:09:15 PM »
These radii are only needed for flexible frameworks, and used as bond-criteria to determine bonding.
For other cases these values do not matter.

j.pu@hotmail.com

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Re: How to define 'radii' in the pseudo_atom.def file
« Reply #2 on: June 12, 2022, 04:04:44 AM »
Dr. Dubbeldam, thanks for your answering.