[gmx-users] Solvent Accessible Area with different Claculation Groups

Petridis, Loukas petridisl at ornl.gov
Mon Dec 21 23:19:48 CET 2009


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 Petridis
Post-doctoral Research Fellow
Center for Molecular Biophysics, Oak Ridge National Laboratory
Building 6011, MS 6309, Oak Ridge, TN 37831
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