[gmx-users] lifetime between pairs of vectors

[David van der Spoel]

Jian Dai wrote:
> Hi, GROMACS users:
> I'm trying to calculate the lifetime distribution between pairs of vectors.
> The problem can be simplified as: there are many vectors in any one 
> frame of a MD trajectory, and when one vector is within a cutoff 
> distance with another vector, and their angle is larger than a cutoff 
> angle, they're deemed as a pair. Some pairs may break and reform in a 
> short time and should be considered something like "interrupted HB" as 
> David van der Spoel has discussed.
> This is quite like the calculation of hydrogen bond lifetime, but I 
> haven't figured it out.
> Thank you in advance.

It seems that you would like to have the cross correlation between two 
arbitrary vectors. There is one tool that comes quite close and that is 
the dihedral autocorrelation (g_angle -h). This does not work with 
cutoffs though (as does the g_hbond analysis). If this is really what 
you want then you need to do some programming. The question is (as 
always) what do you want to analyze? What is the physical process and is 
there an experimental reference?
> 
> DJ
> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se