[gmx-users] FEP and excluded atom interactions

Nuno Micaelo micaelo at itqb.unl.pt
Fri May 21 16:58:09 CEST 2004

Dear gmx developers

I would like to repost a question that had no answer yet.

As far as I know, the question is relevant in the design and capability
of performing certain FEP simulations using GROMACS.

In my particular case, the perturbation can be schematically defined as:

State A      ->  State B

R1-O1-O2-R2  ->  R1-O1   O2-R2

The difference between state A and state B is the *disappearing* bond between
both O atoms.

In the Gromacs User Manual, Table 5.4 it says that exclusions can not be
With no perturbation of the exclusions, in state B, the O1 atom and O2
atom do not interact because they are previously excluded in the initial
However, i would like that a non-bonded interaction between the O atoms
exist in the final sate.
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?

Thanks in advance

Micaelo, NM

Instituto de Tecnologia Química e Biológica
Protein Modeling Group

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