[gmx-users] g_sas

[David van der Spoel]

On 2010-04-04 07.13, Chih-Ying Lin wrote:
>
> HI
> THe command =>
> g_sas_mpi -f 6LYZ-MD566500.xtc -s 6LYZ-MD566500.tpr -o
> solvent-accessible-surface.xvg -oa atomic-sas.xvg -or residue-sas.xvg
>
>
>
> In the solvent-accessible-surface.xvg =>
> @ s0 legend "Hydrophobic"
> @ s1 legend "Hydrophilic"
> @ s2 legend "Total"
> @ s3 legend "D Gsolv"
>
> What does "Hydrophobic" mean here?
> What does "Hydrophilic" mean here?
> Does "Total = Hydrophobic+Hydrophilic" ?
> What does "D Gsolv" mean here?
> How can Gromacs define "Hydrophobic atoms" and "Hydrophilic atoms" ?
>
DG solv is computed according to Eisenberg et al. See scree output for 
reference.

Hydrophobicity is determined from the charge of an atom, not a very good 
method maybe, there you can supply an index file to determine which 
residues are hydrophobic yourself.
>
>
> What does the Area unit mean ? => "Area (nm\S2\N)"

How about square nanometer for an area?

>
>
> Thank you
> Lin
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se