GROMACS version: 2019.3
GROMACS modification: No
Hi, I’m trying to calculate the sasa of a single atom in my protein from a trajectory of the protein. Here is my command:
gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_S_atoms_only.ndx -o sasa_test.xvg -surface protein -output a_737
For some reason, the sasa values I get from this command are always identical to the sasa values for the entire protein (i.e. when I set output to protein).
Is there something wrong with my command line?