[gmx-developers] Exclusions

[Ana Sofia]

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
states.

How can redife my exclusions?

thanks in advance,

Sofia Oliveira


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Ana Sofia F. Oliveira
PhD Student
Instituto de Tecnologia Química e Biológica (ITQB)
Universidade Nova de Lisboa
Avenida da República, EAN
Apartado 127
2780-901 Oeiras
Portugal

Email: asfo at itqb.unl.pt or asfoc at iol.pt
Phone: (+351) 214469613
Fax: (+351) 214411277
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