[gmx-users] g_sas question

Eric Smoll ericsmoll at gmail.com
Tue Jan 20 02:27:11 CET 2015


I am using the Gromacs 4.6.5 g_sas tool with custom radii for each atom as
specified with a local vdwradii.dat file.

Are the surface areas reported in "-or atomarea.xvg" on a sphere defined by
R_VDW or at R_VDW + R_probe?

Similarly, is the "-minarea #" flag a threshold value that applies to
surface areas defined by R_VDW or R_VDW + R_probe? I assume that "-minarea
#" simply filters the values output by "-or atomarea.xvg" to determine if
the atom is a surface atom or not.


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