[gmx-users] Surface area calculation

[XAvier Periole]

reference:
Eisenhaber F, Lijnzaad P, Argos P, Sander C, & Scharf M (1995) J.  
Comput. Chem. 16, 273-284.

On May 11, 2011, at 2:34 PM, Laura Leay wrote:

> 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.
>
> 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.
> < 
> area 
> .xvg 
> > 
> < 
> atomarea 
> .xvg 
> > 
> < 
> conf 
> .gro 
> > 
> <grompp.mdp><methane.itp><resarea.xvg><topol.top><PIsurfaceOPLS.f90>--
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