[gmx-developers] Re: g_sas difference between 4.0.7 and 4.1(4.0.99_development_20090425)/4.5.2

[David van der Spoel]

On 2011-04-08 20.02, Ilya Chorny wrote:
> Can anyone point me to the changes that were made for g_sas between
> 4.0.7 and 4.5? I get different results (see below).  I read through the
> bug and revision history and could not find anything.

I fixed bug 180
http://redmine.gromacs.org/issues/180

commit 3cd2e6bc5c00a84d66994de8d2eada4b52c5ab27
Author: spoel <spoel>
Date:   Thu Feb 28 11:54:46 2008 +0000

     Fixed bug 180

After that there is this comment:
commit 4278585fb7b8908959c0f40ce44c3dfece4fa0d4
Author: Berk Hess <hess at csbl10.cbr.su.se>
Date:   Fri Jun 26 16:55:57 2009 +0200

     fixed incorrect connelly surface with pbc

Strangely, 4.0.7 has a date of 2009-12-06, whereas the version that you 
point to has a date of 2009-04-25. It could therefore be that the fix 
was never applied in the 4.0.x branch but it was in the head branch.
If you *really* want to know you could cherry-pick these commits and 
apply them to the release-4-0-patches branch.

Otherwise the general problem with this code is that the PBC support was 
hacked in by me at some stage, but no other SAS code that I know of can 
deal with PBC. For molecules without PBC g_sas gives roughly the same 
results as MSMS.

>
> g_sas 4.0.7:
> @ s0 legend "Hydrophobic"
> @ s1 legend "Hydrophilic"
> @ s2 legend "Total"
> @ s3 legend "D Gsolv"
>           0     119.157     115.294     234.451    -586.244
>
>
> g_sas 4.1(4.0.99_development_20090425):
>
> @ s0 legend "Hydrophobic"
> @ s1 legend "Hydrophilic"
> @ s2 legend "Total"
> @ s3 legend "D Gsolv"
>           0     99.1454     107.813     206.958    -517.304
>
> g_sas 4.5.2
>
> @ s0 legend "Hydrophobic"
> @ s1 legend "Hydrophilic"
> @ s2 legend "Total"
> @ s3 legend "D Gsolv"
>           0     99.1454     107.813     206.958    -517.304
>
>
> --
> Ilya Chorny Ph.D.
>


-- 
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