GROMACS version: Any
GROMACS modification: No
Hello everyone,
I am planning to run a simulation to study the interaction of an organic anion near a surface step defect. However, I’ve been considering some potential issues and how to handle them, and I would appreciate insights from more experienced researchers (as I’m relatively new to MD simulations).
My initial thought was to add a counterion to neutralize the simulation box. However, this raises a few concerns:
Including an ionic pair in the system would create a dielectric dipole, which could interact with its periodic images.
I am using metadynamics to calculate the PMF, and having a free counterion could significantly slow convergence. This is because the ion would need to explore all possible positions that could influence the molecule–surface interaction. One way to address this might be to restrain the ion to a region of the box where it doesn’t interact with the molecule near the step defect, but this wouldn’t solve the dipole issue.
I’ve seen similar simulations (e.g., https://doi.org/10.1021/acs.cgd.1c01414) that use only a single ion. Although it’s not explicitly mentioned in that paper, I believe they apply a background charge correction—this is referenced in another paper on ion–surface adsorption (https://doi.org/10.1021/ja204714k), where they mention automatic charge correction for periodic calculations. So, while avoiding an explicit counterion might eliminate dipole formation from ionic pairs, wouldn’t a uniform background charge combined with a mobile ion still generate a dipole? Or am I missing something fundamental about how background charge corrections work?
Another possibility is to include the counterion along with a finite concentration of salt. However, I would prefer to first analyze the molecule–surface interaction in isolation, without external effects from solution ions.
I would greatly appreciate any suggestions or feedback on how to best approach this!
Thank you in advance!