diff --git a/_lessons/Introduction.md b/_lessons/Introduction.md index 8f387dd..93f458e 100644 --- a/_lessons/Introduction.md +++ b/_lessons/Introduction.md @@ -44,8 +44,8 @@ can usually be set up without these assumptions, but we'll make these assumption - Harmonic bond angle terms - Periodic dihedral terms - Non-bonded terms made up of point charges and Lennard-Jones repulsion/dispersion terms - - constant temperature is maintained: (see below)[fun-facts-from-the-free-energy-difference-definition] - - **Masses do not alchemically change.* If one wishes to do this, substitute all potential energies, $U$, with the more general Hamiltonian, $\mathcal{H}$. + - **constant temperature is maintained** during the alchemical change (see below for more information)[fun-facts-from-the-free-energy-difference-definition] + - **Masses do not alchemically change.** If one wishes to do this, substitute all potential energies, $U$, with the more general Hamiltonian, $\mathcal{H}$. - **QN and QM/MM** will **not be considered** there are number of other more complicated factors to consider that are beyond the scope of this discussion. ### Free Energy Difference Equation