[gmx-users] allosteric effect

[Qasim Pars]

Dear gmx users,

The protein I have simulated over 200 ns with GROMACS is dimer and shows
positive allostery. Based on experimental data, the second ligand of
protein has greater binding affinity than the first ligand. I would like to
prove the positive allosteric effect of protein by some analyses. But I
really don't know which analyses helps me to investigate/look into the
allosteric effect. Could you please suggest me some useful analyses to
investigate the allosteric effect (except for RMSD, RMSF)? I have
simulations for singly liganded, doubly liganded and apo state.

Thanks a lot, in advance.
-- 
Qasim Pars