How to obtain the charge of each atom of MOFs?

peteboyd / lammps_interface

automatic generation of LAMMPS input files for molecular dynamics simulations of MOFs

MIT License

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How to obtain the charge of each atom of MOFs? #12

Closed pincher-chen closed 5 years ago

pincher-chen commented 5 years ago

Hi,

I want to use UFF4MOF to simulate my model, but I found the charges of MOFs are not assigned by lammps_interface.py. A method is mentioned in paper of Journal of Computational Chemistry, Vol. 11, No. 4, 431-439 (1990) . Here, if i get charges by method of quantum chemistry, I am wondering how lammps_interface.py writes charges to data file of lammps. Can you give me some tips?

askforarun commented 5 years ago

quick and dirty solution: Cut the "Atom section" paste in to matlab as a matrix say A Open matlab Charge= [....] Then A(:,3)=charge;

Elegant solution: grep, bash, awk, sed

peteboyd commented 5 years ago

Hi, If you have partial charges for each atom, you can enter them as a new column in the .cif file as '_atom_type_partial_charge' in the atom block.