Hi,

We are examining a system comprising of two molecules (called mol1 and mol2)  
in water that are initially separated by > 1.5nm. We calculate the surface 
accessible area of the first molecule ( mol1) in two ways:
(a) sasa_a: by setting both the output and calculation groups to mol 1 
(b) sasa_b: setting the calculation group to mol1 and mol2, and output group to 
mol1
During the simulation, the molecules are separated by more 1.5nm and since the 
probe radius = 0.14nm, we expected the values of the two surface areas to be 
identical. Instead we found sasa_a and sasa_b to differ by about +- 1.5 nm^2. 
Although this variation is small compared to the mean value ~86 nm^2, it has 
caused us some concern. We were also surprised that sasa_b was larger than 
sasa_a for part of the simulation. (The same trend is observed when the 
accuracy of the calculation was increased by using ndots=48).

I was wondering if anyone has some insight on why the two sasa values are not 
identical.

I am attaching a figure displaying the calculations described above, obtained 
by:
g_sas -f /traj-0-37 -s top.tpr   -n index-1-2.ndx -b 0 -e 100 -ndots 24

Many thanks for your help,

Loukas

Loukas Petridis
Post-doctoral Research Fellow
Center for Molecular Biophysics, Oak Ridge National Laboratory
Building 6011, MS 6309, Oak Ridge, TN 37831
865-576-2576 
http://cmb.ornl.gov/people/lpk 

<<attachment: sasa.png>>

<<attachment: mindist.png>>

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