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
er...@xray.bmc.uu.se 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/Support/Mailing_Lists/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/Support/Mailing_Lists
