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* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
