Calculation of the solvent accessible surface area

User discussions
1

GROMACS version: 2018.1
GROMACS modification: No
hi everyone, I am calculating the SASA for my solvated small molecule and for one atom of that small molecule using -surface ‘small molecule’ -output ‘atom of small molecule’ as options in the sasa command and I get:

  0.000    3.781    0.038
  0.000    3.695    0.038
  0.000    4.008    0.038
  0.000    3.912    0.038
  0.000    4.204    0.075
  0.000    3.963    0.038
  0.000    4.004    0.038
  0.000    3.748    0.000
  0.000    3.777    0.000
  0.000    4.356    0.113
  0.000    3.857    0.038
  0.000    3.842    0.000
  0.000    3.924    0.038
  0.000    3.732    0.038
  0.000    3.699    0.000
  0.000    3.558    0.038
  0.000    3.819    0.000
  0.000    4.091    0.000
  0.000    3.937    0.000
  0.000    3.869    0.000
  0.000    4.035    0.000

the first column is time, the second is the SASA for the small molecule and the third is SASA for the atom. It is not clear to me why the atom’s SASA is always a multiple of 0.038 (0, 0.038, 0.075, 0.0113). The SASA of the atom always takes one of these discrete values for the entire MD simulation. I noticed the same thing for another atom of that small molecule.

Is this an indication that I am running the sasa command wrong? Is this an effect of the use of a grid in the calculation of SASA? (I do not know the algorithm used)

Thank you.