[gmx-developers] Re: [gmx-users] programming gromacs -> WHAM ?

David spoel at xray.bmc.uu.se
Sun Jan 18 08:50:15 CET 2004

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 compareable with umbrella sampling results.

What's wham? There is a tool called g_wham which does Widom particle

> 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
> 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

> 3) any answers to the questions in my previous mail, concerning
> structure/hirarchy of subroutines, definition and sope of variables
> and pointers, etc. in particular in the context of the umbrella
> sampling
> bit of the code would be very helpful.
As I said, there isn't much, except a tiny bit in the users manual.
We have been considering using doxygen for automatic documenting. As a
matter of fact this was also initiated by Justin.
> cheers,
> Michael
> ______________________________________________________________________
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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