All calculations were performed using the Sander module in the AMBER8(47 ) package that was modified to carry out the accelerated MD simulations. The GAFF force field was used to describe the solute in all simulations. The butane molecule was solvated in a periodic box of explicit TIP3P waters,(48 ) which extends on each side 10 Å from the closest atom of the solute, by using the Leap module in AMBER. To bring the system to its correct density, we carried out an MD simulation for 1 ns in which the NPT ensemble (T = 300 K, P = 1 atm) was applied. All data collection was carried out over MD simulations of 1 ns, during which the NVT ensemble (T = 300 K, density= 0.984 g/mL) was applied. The final configuration was then used as the starting point for the propane → propane simulations. In both systems, butane and propane → propane simulations, each solute atom was assigned with zero partial charge. The free energy change was calculated by varying λ form 0 (initial state) to 1 (final state). All TI simulations were carried out using seven discrete points of λ, which were determined by Gaussian quadrature formulas. Normal and accelerated MD simulations of 500 ps were carried out for each λ point. The NVT ensemble was used in all TI simulations. Temperature and pressure were controlled via a weak coupling to external temperature and pressure baths(49 ) with coupling constants of 0.5 and 1.0 ps, respectively. Apart from all TI simulations where the time step was set to 1 fs, the equations of motion were integrated with a step length of 2.0 fs using the Verlet Leapfrog algorithm.(50 ) For further analysis, the trajectory was saved every 1.0 ps. The PME summation method was used to treat the long-range electrostatic interactions in the minimization and simulation steps.51 ,52 The short-range nonbonded interactions were truncated using a 8 Å cutoff, and the nonbonded pair list was updated every 20 steps.