Why is the gibbs free energy from gmx sham positive

User discussions
1

GROMACS version: gmx sham, 2023.1-conda_forge
GROMACS modification: No

Hello everyone

I used gmx sham to want to draw Free Energy Landscapes information.

In Gibbs.xpm generated by the program, I see that the energy unit is “G (KJ/MOL)”, and the value corresponding to the lowest position of free energy can be 0. The free energy in other places is positive value.

Usually the free energy I understand is negative. What free energy units can be dedicated here, and how to understand why the free energy of most locations can be positive?

2

You need to consider what the free energy landscape means in this case. The free energy is not an absolute value. In this case it is relative to the lowest free energy in the output (0). So, you could consider the free energy a measure of the probability of going from the most favourable state (lowest free energy) to other states in the free energy landscape.