How to measure discrete charge-charge interactions

GROMACS version: 2019.1
GROMACS modification: No
Here post your question

Hi there, I have currently used rmsd, rdf, gyr basic functions to analyse shift/movement of a particular atom respective to another (or residue/protein to another molecule excluding water interactions…).

Log file has various different energy profiles. Can this be used to measure discrete charges on a particular atom’s of a two adjacent species?

Is there a GROMACS toolset that is available to measure and analyse a non-bonded (bonded) discrete charge-charge interactions by particular pair of atoms using a md-run trajectory?

Is there a simple way to achieve such energy interactions?

You can use energygrps in the .mdp file, regenerate a .tpr file and use mdrun -rerun to compute interaction energies, but specific atom-atom electrostatic interactions will have no physical meaning (nor would even the sum of electrostatic interactions on a given group, because no force field is parametrized in such a way that this quantity is meaningful).

1 Like