We are interested on the DNA damage induced by ionizing particle, specifically, heavy charged particles. We are exploring the capacity of classical molecular dynamics for studying the interaction of energetic protons and other heavy charged particles with the DNA.
In this project, the reax force-field has been adjusted for the case in which a swift proton interacts with five important atoms present in organic molecules, namely C, O, H, N, and P. Specifically, the non-bonded van der Waals potential has been fit, using reference values determined by the Time Dependent Density-Functional Theory. The Octopus code has been used for TD-DFT calculations. In addition, the source piece of code reaxc_ffield.cpp has been adapted to account for a new species called X, that represents the proton. This code and the file with the corresponding force-field parameters can be found here:
The user should replace the reaxc_ffield.cpp file and resintall the LAMMPS code in order to use the associated ffield_protein_short_range.txt file that contains the field parameters.
