[gmx-developers] g_hbond development

[Erik Marklund]

Having recently made a bunch of changes in g_hbond (and comitted it to the cvs repository), I have discovered that the -ac option still isn't working properly in conjunction with the -contact option. The problem is not just a programming error, but actually insuficient theory/phonomenology. When analyzing h-bonds everything is fine. Forward and back rate constants are calculated for the reaction A <=> B, where A = 'h-bonded' and B = 'within cut-off but not h-bonded'. For contacts, however, A is 'within cut-off range R', but how should B be defined? One possibility is to use B = !A, which doesn't follow the theory being described in Luzar 2000 and that is used in the present code for h-bonds. Another possibility is to define a second cut-off range R2 and say that B = 'within R2, but not within R'.

I have posted a bugzilla (#88) and hope to resolve this issue all by myself this week. However, any suggestions or wise comments are more than welcome. This is the stratregy I have decided to go for:

- introduce option -R2, being the second cut-off (see above)
- add an additional array to the t_hbond structure containing contacts within R2, similar to g[] (see code).
- if -R2 is positive and -contact and -ac flags are set, calculate the autocorrelation stuff using the second definition of B above.
- if R2 is zero, B is defined as !A and the autocorrelation stuff is calculated accordingly.

Using -R2 will obviously require more memory. Hopefully this will not be a big problem.

When done I will of course commit these new features/bugfixes to the cvs repository. And as I mentioned previously I'll be glad to recieve suggestions and comments, but please send them soon, for I'll go on vacation this sunday.

/Erik Marklund
-- 
Erik Marklund, PhD Student, Molecular Biopcysics group,
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
erikm at xray.bmc.uu.se
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20060626/ce1d924e/attachment.html>