1. Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy 
Jessica M.J. Swanson, Richard H. Henchman, J. Andrew McCammon 
Biophysical Journal 
Volume 86, Issue 1, Pages (January 2004)
DOI: /S (04)
Copyright © 2004 The Biophysical Society Terms and Conditions

2. Figure 1
(a) The protein's solvation energy (light gray) and molecular mechanics energy (dark gray) across 3ns of simulation. The darker solid and dashed lines represent a 100ps running average. (b) The protein's total energy, ETOT=UMM+WPBSA, and running average.
Biophysical Journal  , 67-74DOI: ( /S (04) )
Copyright © 2004 The Biophysical Society Terms and Conditions

3. Figure 2
The change in free energy (EAB-EA− EB) of each snapshot for (a) the separate and (b) the single simulation evaluations. The lightest shade is the molecular mechanics energy, the middle is the solvation energy, the darkest is the total, and the smooth black line is a 100-frame running average of the total energy.
Biophysical Journal  , 67-74DOI: ( /S (04) )
Copyright © 2004 The Biophysical Society Terms and Conditions