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

Justin A. Lemkul jalemkul at vt.edu
Tue Dec 22 00:09:18 CET 2009

Petridis, Loukas wrote:
> 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.

 From g_sas -h:

"The calculation group should always consists of all the non-solvent atoms in 
the system. The output group can be the whole or part of the calculation group."

So, setting the calculation group to only include "mol1" is simply incorrect 
usage of the program.


> 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 
> ------------------------------------------------------------------------
> ------------------------------------------------------------------------


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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