Free-energy calculations - Theoretical Biophysics Group

Free-energy perturbation calculations “Alchemical transformations”
30 JORGENSEN, RAVIMOHAN (1985); PEARLMAN (1994)
31 JORGENSEN, RAVIMOHAN (1985)
In the single-topology paradigm, a common topology is
sought for the initial state and the final states. 30
The most complex topology serves as the common denominator
for both states, and the missing atoms are
treated as vanishing particles, the non–bonded parameters
of which are progressively set to zero as λ varies
from 0 to 1.
Example: In the mutation of ethane into methanol, the
former serves as the common topology. 31 As the carbon
atom is transformed into oxygen, two hydrogen atoms of
the methyl moiety are turned into non–interacting, “ghost”
particles by annihilating their point charges and van der
Waals parameters.
Chris Chipot Free-energy calculations