[gmx-users] FEP and excluded atom interactions

Nuno Micaelo micaelo at itqb.unl.pt
Fri May 7 10:58:01 CEST 2004

I would like to do a FEP using Gromacs. 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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