[gmx-users] Nonbonded 1-4 interactions

[Mark Abraham]

Santanu Chatterjee wrote:
> Hi,
>     I am somewhat new to gromacs. I am trying to understand how Gromacs 
> estimates scaled nonbonded 1-4 LJ interactions.
> I learned from the manual that if gen-pairs = yes, gromacs uses the 
> general combination rule for nonbonded 1-4 LJ interaction
> with the factor fudgeLJ.  But does Gromacs calculates the scaled 1-4 LJ 
> interaction for all 1-4 pairs in the molecule? Or does it
> do it only for the entries under the [pairs] section in topology file? 
> And what about Coulomb interactions?

See manual 5.3.4 and 5.7.1, and probably others.

Mark