What is the nature of H-bonding in GROMACS ? Is it primarily electrostatic , or does it calculate the number of H-bonds based on the angle and distance criteria?
Can i relate the electrostatic interaction to H bonding?
(I used the CHARMM36 force field for my MD simulation)
There isn’t any command that relates the h-bonds to electrostatic interactions directly (at least not one I could find), but what you could do is use the hbond -hbn flag to retrieve an index file of all the atoms involved with hydrogen bonding, as is done in this tutorial (How to study Hydrogen bonds using GROMACS - Compchems) than use that index file to specify the atoms to be used as the energy groups when extracting information on electrostatic interactions using gmx energy, similar to the analysis done in this tutorial (Protein-Ligand Complex)