[gmx-users] interaction energy

[maryam haji]

Dear gromacs users

My system contains protein and CNT and water molecules.

I want to obtain interaction energy. There is following equation in some
papers:

E(int) = E(cnt+protein) - E(cnt) - E(protein).

Based on this equation, should 3 MD simulations?

1-  cnt in water

2- protein in water

3- protein and cnt in water

I have 3 questions:

1) Is my opinion true?

2) What means of E(x)? Are E(cnt) and E(protein) corresponded to total or
potential energy
of cnt and protein in simulation # 1 and 2?

3) Is E(cnt+protein) corresponded to total potential energy
of cnt+protein in simulation #  3 ?


Thanks in advance