updated README

Author: wagleswapnil

README.md

@@ -1,11 +1,15 @@
 # waterNES
-This repository contains workflows to calculate relative free energies
-(RBFE) between ligands that bind to target protein with different numbers of
-trapped water molecules. The RBFE is calculated
-using non-equilibrium switching for buried water molecules. These
-workflows operate on thermodynamic cycles like these:
-
-![Thermodynamic cycle](https://github.com/MobleyLab/waterNES/blob/main/docs/ThermodynamicCycle.png?raw=true)
+This repository contains workflows to:
+1.  calculate absolute binding free energies of trapped waters in proteins/protein-ligand complexes using
+the following thermodynamic cycle
+![Thermodynamic cycle](https://github.com/MobleyLab/waterNES/blob/main/docs/abfe_cycle_full.png?raw=true)
+2. calculate relative free energies (RBFE) between ligands that bind to target protein with different numbers of
+trapped water molecules. The RBFE is calculated using non-equilibrium switching (NES) for trapped water molecules
+and implements the following thermodynamic cycle
+![Thermodynamic cycle](https://github.com/MobleyLab/waterNES/blob/main/docs/rbfe_cycle_short.png?raw=true)
+3. to calculate RBFEs between ligand pairs with different numbers of trapped water molecules and implementing 
+a fully NES-based workflow, using thermodynamic cycle
+![Thermodynamic cycle](https://github.com/MobleyLab/waterNES/blob/main/docs/NES-Total-Chemdraw.png?raw=true)
 
 The purple cycle includes additional restraints for the protein, and
 is preferred when it is likely that the binding site might collapse