[gmx-users] FEP and excluded atom interactions

[Marc Lensink]

Quoting Nuno Micaelo <micaelo at itqb.unl.pt>:

> State A      ->  State B
> 
> R1-O1-O2-R2  ->  R1-O1   O2-R2
> 
> So, how do i fix this? How should the FEP be done in order to
> ensure that both O atoms *do not* have their non-bonded interactions
> excluded in state B?

This is potentially very complicated stuff. Perhaps you could model the
non-bonded state by a very weak force constant. Check J. Comput. Chem. 20
(1999), 886-895 (and a section in J. Phys. Chem. B. 108 (2004), 5483-5488).

Marc