[gmx-users] Surface area calculation
erikm at xray.bmc.uu.se
Wed May 11 15:48:36 CEST 2011
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,
> 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.
> 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
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/
More information about the gromacs.org_gmx-users