[gmx-developers] programming gromacs -> WHAM ?

Michael Brunsteiner mbx0009 at yahoo.com
Sun Jan 18 20:58:34 CET 2004

dear David,

thanks for your help; below a few more comments ...

--- David <spoel at xray.bmc.uu.se> wrote:
> On Sun, 2004-01-18 at 00:24, Michael Brunsteiner wrote:
> > dear all,
> >  
> > As stated in my previous mail (programming gromacs)
> > I'd like to try tinkering with the source code.
> > More to the point I'd like to see a tool doing WHAM
> > or anything compareablek with umbrella sampling results.
> What's wham? There is a tool called g_wham which does Widom particle
> insertion

WHAM is the acronym for "weighed histogram analysis method",
(S. Kumar, D. Bouzida, R. H. Swensen, P. A. Kollman, and J. M. 
Rosenberg. J. Comp. Chem., 13:1011-1021, 1992.)
a method for efficient (post)processing of umbrella
sampling results, giving a free energy profile with
minimized statistical uncertainties.
The acronym is commonly used nowadays, but maybe you 
know the method under a different name ...

> > Before starting to look into the code I'd appreciate if you
> > guys could provide me with some information:
> > 1) what is the current state of the umbrella sampling code,
> > and more generally, the pull code ?
> It  *should* work in gromacs 3.2

fine, I downloaded 3.2beta about two weeks ago, how close
to a proper release version is that ?

> > 2) I understand that a gentleman called Justin MacCallum 
> > worked on the pull code at some point. The link to his site 
> > given in the developers FAQ is dead. Is Justin still around
> > or is anybody else working on the pull code, and if so who ?
> He's in Peter Tielemans group

I'll try contacting him. If the pull code is really working
in 3.2 then it should suffice to write another analysis tool
for my purposes, this should be easier than tinkering with the
main code and I might be able to do that without too much help ...


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