[gmx-users] How to turn 1-3 interactions on?

[Jianwei Wang]

Hello, 

This has something to do with exclusion list.
I have a special need and have to turn 1-3 interactions on, that is, I 
need nobonded interactions (vwd and electrostatic) included in energy 
calculations for atoms more than one bond away. I have tried the 
following, seems gmx still excludes 1-3 interactions because I have atom 
close contacts (less than 0.1 Angstroms)and like-charged atoms looking to 
each other, and my system stalls: 
(1) assign nrexcl with  1 in [ moleculetype ]
(2) all bonds use function type 6 
(3) what else?
Best,
Jianwei