How to use umbrella sampling and WHAM for free energy calculation when pull code was not applied.
I used the enforced rotation method (Kutzner et al., 2011) to rotate a domain within a protein. Next, 120 windows were extracted from the generated trajectory and simulated separately.
Enforced rotation generates lots of data that is written in several files. What should be used for free calculations and how to run WHAM with these files?
All the best,