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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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