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

David van der Spoel spoel at xray.bmc.uu.se
Tue Dec 22 08:36:51 CET 2009

Justin A. Lemkul wrote:
> 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'm not sure this is correct actually (although there has been a bug in 
the program for a long time). But if you want to e.g. compute the 
occluded area in a protein-protein interaction you  have to compute A+B-AB
where A is the area of just protein A, ignoring everything else and so 
on. The fact the OP does not get the same area (did he use the same 
molecules?) is probably just poor sampling. Just wait a couple of 
hundred nanoseconds and see whether the distributions overlap.

> -Justin
>> 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
>> ------------------------------------------------------------------------
>> ------------------------------------------------------------------------

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list