Hi,
The usual way is to build a topology whose A and B states are the mutated
forms, and you then equilibrate the system separately at each lambda point
interpolating between them. You "simply" need a starting configuration with
a plausible geometry for each such point.
Mark
On Mon, Feb 15, 2016 at 9:27 PM Jagannath Mondal
wrote:
> Dear Users
> I want to compute the relative free energy for mutating one residue of a
> protein to another one using free energy perturbations as implemented in
> gromacs. I wanted to know how I can generate the starting configurations of
> the intermediate lambda values. Is there any interpolation scheme within
> gromacs that will let me generate the intermediate structures.
> Jagannath
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