[gmx-users] free energy of complex system

abhisek Mondal abhisek.mndl at gmail.com
Wed Aug 29 07:55:37 CEST 2018

I'm just trying to calculate free energy of a complex system using
following method:

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*


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