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.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
