[gmx-users] Long distance effects of mutation and stability

[Jorge Fernández de Cossío Díaz]

I want to analyse the effects of a point mutation in a protein. The protein
is 150 amino acids long.

I have experimental evidence that a mutation has a distant effect in the
protein. More precisely, the mutation affects the binding of the protein to
another partner, even though the mutation occurs far from the binding site
(almost on the opposite side).

I don't know if the mutation is affecting the overall folded state, or if
it has a long-range effect locally on the binding site.

I have two broad questions:

1) Can GROMACS help me to answer this question? More precisely, are there
papers published that use GROMACS to study stability effects of mutation,
or long-range effects?

2) How long should I run the simulation to see long-range effects?
Currently I have a 100ns simulation. In your experience, is this enough?