[gmx-users] lifetime of hydrogen bond

[spss4 at iacs.res.in]

  Thank you for your suggestion.
----- Message from David van der Spoel <spoel at xray.bmc.uu.se> ---------
    Date: Thu, 2 Jan 2020 08:28:17 +0100
    From: David van der Spoel <spoel at xray.bmc.uu.se>
Reply-To: gmx-users at gromacs.org
Subject: Re: [gmx-users] lifetime of hydrogen bond
      To: gmx-users at gromacs.org

> 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at  
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before  
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests  
> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or  
> send a mail to gmx-users-request at gromacs.org.

----- End message from David van der Spoel <spoel at xray.bmc.uu.se> -----