Gromacs users, I have 3 easy questions regarding the use of g_sas
1) I am trying to understand exactly how gromacs computed the SAS. I looked at vdwradii.dat and it says ; Very approximate VanderWaals radii ; only used for drawing atoms as balls or for calculating atomic overlap. Does atomic overlap include SAS calculations? If not, where does g_sas get the sphere sizes when making the calculation? 2) How can I tell gromacs to look at a different file for atom sizes? I would like to compare the SAS for a C-alpha model with varying sizes for the CA beads. 3) How goes g_sas determine which atoms are hydrophobic and hydrophilic? I would like to call some CA atoms hydrophobic and others hydrophilic. Thanks in advance! -Paul
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