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