[gmx-users] LINEAR INTERACTION ENERGY

[Vytautas Rakeviius]

Basically you do two MD runs one with ligand in water other with ligand in protein. You must set proper energygrps in mdp file so you get 2 edr files from runs and in the end you use "gmx lie" (http://manual.gromacs.org/programs/gmx-lie.html) to compute difference between those two edr files.You might check this paper too:
Curr Comput Aided Drug Des. 2015;11(3):237-44. 

    On Thursday, March 16, 2017 12:15 PM, Kulkarni R <alumniphysics at hotmail.com> wrote:
 

 Hi gromacs users,

In order to calculate delta G (Gibbs free energy) for protein ligand binding, what are the steps to be followed in Linear interaction energy?


Are there any tutorials for the same?


Thanks,

Kulkarni.R
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