What Prob size is better for gmx SASA?

User discussions
1

Dear all,

I want to calculate solvent accessible surface area using gmx sasa. The probe size is 0.14 nm by default. Do I have to change probe size to 0.315 ( sigma of Tip3p Oxygen)?
When I changed it to 0.315 the average SASA is around zero. But, when I use default size it is about 200 nm^2. Which one is true?

Thanks alot

2

The actual radius of a water molecule is 0.14 nm, which is why that is the default and it is the value you should use. The value of σ is a force field-dependent quantity and represents the distance at which the LJ potential is zero between two atoms. It is not the size of the atom/molecule.