[gmx-users] Re: Calculations of area per lipid using g_sas
Mark.Abraham at anu.edu.au
Tue Jul 10 07:55:29 CEST 2007
Hwankyu Lee wrote:
> Dear Mark,
> I just measured the projected XY-area (simply XY-size of box), and used
> typical periodic boundary condition (In g_sas, default considers PBC).
> In the small system (128 lipid bilayer), there is no undulation, so
> projected area per lipid may be almost the same as non-projected area
> per lipid. So, total solvent accessible surface area (the third column)
> should be always larger than the projected XY-area, but I observed that
> total SASA become smaller than the projected XY-area at some point.
> Could you give me some suggestions?
Show us your box dimensions at a point when you observe this to occur -
or preferably a relevant chunk of both g_sas and g_energy output.
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