AMBER Free Energy Tools: A New Framework for the Design of Optimized Alchemical Transformation Pathways

Hsu Chun Tsai, Tai Sung Lee, Abir Ganguly, Timothy J. Giese, Maximilian CCJC Ebert, Paul Labute, Kenneth M. Merz, Darrin M. York

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


We develop a framework for the design of optimized alchemical transformation pathways in free energy simulations using nonlinear mixing and a new functional form for so-called "softcore"potentials. We describe the implementation and testing of this framework in the GPU-accelerated AMBER software suite. The new optimized alchemical transformation pathways integrate a number of important features, including (1) the use of smoothstep functions to stabilize behavior near the transformation end points, (2) consistent power scaling of Coulomb and Lennard-Jones (LJ) interactions with unitless control parameters to maintain balance of electrostatic attractions and exchange repulsions, (3) pairwise form based on the LJ contact radius for the effective interaction distance with separation-shifted scaling, and (4) rigorous smoothing of the potential at the nonbonded cutoff boundary. The new softcore potential form is combined with smoothly transforming nonlinear λ weights for mixing specific potential energy terms, along with flexible λ-scheduling features, to enable robust and stable alchemical transformation pathways. The resulting pathways are demonstrated and tested, and shown to be superior to the traditional methods in terms of numerical stability and minimal variance of the free energy estimates for all cases considered. The framework presented here can be used to design new alchemical enhanced sampling methods, and leveraged in robust free energy workflows for large ligand data sets.

Original languageEnglish (US)
JournalJournal of Chemical Theory and Computation
StateAccepted/In press - 2022

All Science Journal Classification (ASJC) codes

  • Computer Science Applications
  • Physical and Theoretical Chemistry


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