[gmx-users] FEP and excluded atom interactions
Marc.Lensink at UGent.be
Fri May 21 18:51:58 CEST 2004
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).
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