[gmx-developers] Exclusions

Berk Hess hessb at mpip-mainz.mpg.de
Fri Mar 30 08:54:42 CEST 2007

Ana Sofia wrote:

>Dear Gromacs-Developers,
>I'm trying to change my system between two states (A and B) by applying
>the TI formalism based on the coupling parameter approach. Since the
>conversion from state A to B involve breaking of a covalent bond between
>two atoms, the excluded neighbours as well as the third neighbours (1-4
>interactions) of these atoms will be different in state A and B.
>As an example: a hexane molecule (state A) is transformed in two propane
>molecules (state B). This implies the breaking of the bond between C3 and
>C4 and the redefinition for state B of all the excluded neighours.
>Apparently, GROMACS does not allow the change in the exclusions between to
>How can redife my exclusions?
>thanks in advance,
>Sofia Oliveira
This issue could be more complicated.
What is your full thermodynamic cycle?

There are two solutions.
One is to remove the exclusions that are going to disappear
and replace them by 1-4 interactions, where you probably
manually have to enter the A and B state parameter to make
them resemble the proper LJ interactions. Also the fudgeQQ
of your force field has to be 1. If your force-field does not
have a fudgeQQ of 1 and your have excluded Coulomb interactions
it will not work.

Another option would be to add all atoms of the B state as virtual
sites, exactly on top of the A-state atoms. You can then make
a separate B-state topology.

Note that you might have trouble sampling at intermediate states,
as the non-bonded and bonded lambda dependencies might
not be well balanced.


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