[gmx-users] Surface area calculation

[Erik Marklund]

Laura Leay skrev 2011-05-11 14.34:
> Can anyone explain in detail the method that gromacs uses to calculate
> surface area? Which surface area is it calculating (e.g., connolley,
> accessible)?
>
> I am under the impression that the final result is given in nm^2. Is
> this correct?
>
>
> Carrying out the surface area calculation in gromacs using the OPLS all
> atom force field I obtain a value of 4.43 nm^2  for methane (carbon =
> opls_138, sigma = 0.35 and hydrogen = opls_140, sigma = 0.25) (CT-HC
> ideal bond length = 0.109, e=284512). The command was
>
> g_sas -f conf.gro -s topol.tpr -oa -or -tv -probe 0.2 -ndots 200 -nopbc
>
> and the result was taken from resarea.xvg
>
>
> I have written a program to calculate the geometric accessible surface
> area using the van der waals radius of the atoms and a probe of a given
> size. The surface is defined from the centre of the probe. Using the
> above values for sigma I obtain a value for methane of 1.15 nm^2 with a
> probe diameter of 0.2 nm.
One difference is that g_sas -probe 0.2 uses a probe with a 0.2 nm 
*radius*, while your code use a 0.2 nm diameter. That doesn't on its own 
explain the difference you report, but you probably want to use the same 
probe when comparing.

Erik
> Obviously the two do not match and I am not sure why.
>
> The individual atom areas for my molecule are:
> C 0.22
> H 0.24
> H 0.23
> H 0.22
> H 0.24
>
> Attached are the files used in the gromacs calculation along with the
> output and my own program. If any one has any suggestions please let me
> know.


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/