[gmx-users] g_sas of ligands

[Steven Neumann]

Dear Gromacs Users,

I am calculating SAS using g_sas of ligands in my system: protein, 30
ligands in water. The hydrophobic SAS of ligands decrease and reach stable
value. Hydrophilic remains stable over the simulation time. I am wondering
whether it  (the decrease o hydrophobic) is because of binding to protein or
aggregations of my small molecules (They do aggregate) or both? I mean: how
is it caculated? Is binding to protein included in the decrease of the
hydrophobic SAS of lignads or it is impossible and  aggregation will be the
one thing?

Thank you,

Steven
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