Free energy difference calculations by thermodynamic integration: Difficulties in obtaining a precise value

Abstract

Free energy difference calculations have been performed by the “slow growth” method of thermodynamic integration of the AMBER 3.0 molecular dynamics program for the mutation of a conformationally restricted threonine dipeptide, N‐acetyl threonyl‐N‐methylamide, to the corresponding alanyl dipeptide. By varying the total simulation length, it has been determined that precise free energy values are obtained only for simulations of greater than 100 ps total simulation time length. By varying the starting configurations for simulations of the same length, it has been determined that averaging the free energies obtained from shorter simulations may not give precise answers. Possible reasons for this behavior are discussed. Copyright © 1991 John Wiley & Sons, Inc.