[gmx-users] Free energy calculations with membrane

[Live King]

Hi everyone,

I am trying to do Justin's thermodynamic integration tutorial with a lipid
bilayer. I believe the energy I will get from this exercise is the energy
required to take alanine from membrane to vacuum. I have placed my alanine
at the center of bilayer. Does this energy output contain contribution from
both alanine-lipid and alanine-water interactions? or just alanine-lipid
interactions.


Thanks,
Vikas