[gmx-users] free energy of complex system

[abhisek Mondal]

Hi,
I'm just trying to calculate free energy of a complex system using
following method:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html

However, I'm facing some difficulties understanding how can I achieve the
goal. The tutorial goes on with a single entity from lambda=0 to 1 with
0.05 spacing for data collection.

Now, if I would like to calculate free energy of a complex (say, dimeric
protein) then how am I supposed to design the lambda states ?
I mean will it be like, one monomer will remain constant and the other
monomer goes from lambda=0 to 1 state ? If that be the case then please
suggest a way to customize the procedure.

Please provide some suggestions.
I'm really willing to apply this method in my scenario.
Thank you.
-- 
Abhisek Mondal

*Senior Research Fellow*
*Protein Crystallography Group*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*