[gmx-users] Re: Calculations of area per lipid using g_sas

Mark Abraham 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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