[gmx-users] g_sas and g_rdf

Kay Gottschalk kay.gottschalk at weizmann.ac.il
Mon Jun 23 18:08:03 CEST 2003

I am trying to look at the radial distribution function of water around 
the surface of my protein. For this I extracted the surface atoms with 
g_sas -i and converted the surfat.itp to an index file. Then I 
calculated the rdf of the solvent with respect to the so determined 
surface atoms. Shouldn't the rdf look similiar to that of water against 
water? It actually looks quite different. And I have the impression as 
if only hydrophobic atoms are in surfat.itp, even if I take -qmax 1. 
Any ideas?

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