[gmx-users] Calculations of preferential interaction coefficient

[Apramita Chand]

Dear All,
I want to calculate the preferential interaction coefficient and
subsequently the Gibbs free energy of solvation for protein in water and in
water-co-solvent mixture.
1. According to the equation specified in the literature, if I can generate
a list of no. of solvent molecules (for each local/bulk region) for each
frame using g_select or g_trjconv tool in GROMACS, it will give me nw, nx
for local and bulk regions per frame.For the entire average of the equation
given, can I take these list of values and for each frame, compute the
value of interaction coefficient. Thereby, if I get a list of all such
values for every frame, I can average it to get to the value of
preferential interaction coefficient over all frames.

Is this method correct?

2. In most of the literature, the protein backbone has been considered as
reference group. Is it necessary to take COM of the backbone while giving
g_select/g_trjconv??


Please suggest


Yours sincerely,
Apramita