Optimal pairwise and non-pairwise alchemical pathways for free energy calculations of molecular transformation in solution phase. Journal Article uri icon



  • We estimate the global minimum variance path for computing the free energy insertion into or deletion of small molecules from a dense fluid. We perform this optimization over all pair potentials, irrespective of functional form, using functional optimization with a two-body approximation for the radial distribution function. Surprisingly, the optimal pairwise path obtained via this method is almost identical to the path obtained using a optimized generalized "soft core" potential reported by Pham and Shirts [J. Chem. Phys. 135, 034114 (2011)]. We also derive the lowest variance non-pairwise potential path for molecular insertion or deletion and compare its efficiency to the pairwise path. Under certain conditions, non-pairwise pathways can reduce the total variance by up to 60% compared to optimal pairwise pathways. However, optimal non-pairwise pathways do not appear generally feasible for practical free energy calculations because an accurate estimate of the free energy, the parameter that is itself is desired, is required for constructing this non-pairwise path. Additionally, simulations at most intermediate states of these non-pairwise paths have significantly longer correlation times, often exceeding standard simulation lengths for solvation of bulky molecules. The findings suggest that the previously obtained soft core pathway is the lowest variance pathway for molecular insertion or deletion in practice. The findings also demonstrate the utility of functional optimization for determining the efficiency of thermodynamic processes performed with molecular simulation.

publication date

  • March 28, 2012

Date in CU Experts

  • September 4, 2015 2:15 AM

Full Author List

  • Pham TT; Shirts MR

author count

  • 2

Other Profiles

Electronic International Standard Serial Number (EISSN)

  • 1089-7690

Additional Document Info

start page

  • 124120


  • 136


  • 12