asfo at itqb.unl.pt
Thu Mar 29 17:17:13 CEST 2007
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,
Ana Sofia F. Oliveira
Instituto de Tecnologia Química e Biológica (ITQB)
Universidade Nova de Lisboa
Avenida da República, EAN
Email: asfo at itqb.unl.pt or asfoc at iol.pt
Phone: (+351) 214469613
Fax: (+351) 214411277
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