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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