GROMACS version: 2023
GROMACS modification: No
In many examples, nrexcl is set to 3, which means nonbonded interactions are excluded for bonded 1-2, 1-3 and 1-4 atoms. If require, these interactions can be added back in the [ pairs ] directive.
My question is how does Gromacs decides what is bonded and what not? As I understand, two atoms are considered bonded if they are defined in [ bonds ]. But then is it possible to define an angle in [ angles ] involving three atoms where no bond is defined in [ bonds ]? Are they still considered to be non-bonded, and therefore nonbonded interactions (van der waals + Coulombic) will still be calculated for these three atoms? This despite the fact that they may be closed to one another.
Thank you.