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Update Introduction.md
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mrshirts authored Apr 3, 2024
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Expand Up @@ -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
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