[gmx-users] lifetime of hydrogen bond

[David van der Spoel]

Den 2020-01-02 kl. 07:47, skrev spss4 at iacs.res.in:
> Dear all
> I want to calculate the hydrogen bond lifetime of a dynamic hydrogen 
> bond which stays for say 10 ns (as I have saved the trajectory with 10 
> ps interval).  I am trying to calculate the lifetime of this hydrogen 
> bond by gmx hbond command
> gmx hbond -f traj_nopbc.trr -s md.tpr -n index.ndx -num 
> hbond_G4_N3_131_N3H4.xvg -dist dist_G4_N3_131_N3H4.xvg -ang 
> ang_G4_N3_131_N3H4.xvg -life life_G4_N3_131_N3H4.xvg
> Its give me a "uninterrupted hydrogen bond lifetime" plot which stays 
> for 200 ps. I cannot understand the meaning of this plot. How to explain 
> this 200 ps lifetime?
> Thanks
> sunipa
The -life option does not give you a meaningful answer since it is 
sensitive to small fluctuations. My oldpaper in J. Phys. Chem. B 110 pp. 
4393-4398 (2006) explains it in detail.

You can rerun without -life and with the -ac flag.

-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se