[gmx-developers] Exclusions

David Mobley dmobley at gmail.com
Thu Mar 29 20:36:06 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
> states.

If you really insist on doing things this way, you might be able to
rig up something involving the pairs list to change the B state
interactions relative to the A state. But I am not sure how you'd deal
with the electrostatics... This sounds like it would be really hard.

Are you sure you can't do your transformation without breaking bonds
by changing your choice of reference state or method? For example, you
might imagine mutating both the A and B states to a common reference
state C. For example if I wanted to go from proline to some other
amino acid, I might do it by mutating both of them to glycine rather
than by breaking the extra bond in proline.

Hexane into two propane molecules... Yikes. Sounds like there would be
a QM contribution you would need, unless you are talking about doing
this both in water and in vacuum, or in water and some other
environment. If so, then are you just interested in the difference in
solvation energies or the difference in transfer energies? Then you
could just calculate the solvation free energy of hexane, and the
solvation free energy of propane, and there you'd have it... (for the
solvation case).

Anyway, I suggest thinking about your end goal and coming up with a
cycle which will allow you to get that end goal with out breaking
bonds (i.e. with only atomic deletions or insertions or


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