[gmx-users] How to generate intermediates for alchemy mutation

Mark Abraham mark.j.abraham at gmail.com
Mon Feb 15 21:43:38 CET 2016


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.


On Mon, Feb 15, 2016 at 9:27 PM Jagannath Mondal <jmondal.backup at gmail.com>

> 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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