[gmx-users] free energy of complex system

[Dallas Warren]

What Gibbs energy are you trying to calculate for the system? Of what
process or transformation?

On Wed, 29 Aug. 2018, 3:56 pm abhisek Mondal, <abhisek.mndl at gmail.com>
wrote:

> 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*
> --
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