# [gmx-users] g_hbond

David spoel at xray.bmc.uu.se
Thu Nov 3 18:46:14 CET 2005

```On Thu, 2005-11-03 at 18:40 +0100, Isabella Daidone wrote:
> Hi,
>
> could anybody explain the legend (0,1,2,3,Total) in the output of g_hbond
> in the file nhbdist.xvg (generated with option -nhbdist)?
That's the number of donor-H atoms with that many HBonds. Total should
equal what you get in hbnum.xvg

>
> And sorry for asking again,
> which is the equation in Luzar's article corresponding to the One-way
> life time of HB?
Nothing, or I don't know. Use either the forward/backward rates or the
integral. If something the One-way corresponds to ignoring the bacward
transition which usually does not make sense.

>
> Thanks,
> Isabella
>
> On Mon, 31 Oct 2005, Isabella Daidone wrote:
>
> > Thanks.
> >
> > Could you tell me which is the equation in the article corresponding to the
> > One-way?
> >
> > Thanks (again)
> > Isabella
> >
> > On Mon, 31 Oct 2005, David wrote:
> >
> >> On Mon, 2005-10-31 at 18:21 +0100, Isabella Daidone wrote:
> >>> Hi,
> >>>
> >>> g_hbond gives the following time constants:
> >>>
> >>> Type      Rate (1/ps)  Time (ps)  DG (kJ/mol)
> >>> Forward         0.014     71.914      15.127
> >>> Backward        0.000   68412.782      32.127
> >>> One-way         0.028     36.162      13.423
> >>> Integral        0.004    230.307      18.012
> >>> Relaxation      0.030     33.494      13.233
> >>>
> >>> Could anybody tell me to which of the time constants mentioned in the
> >>> Luzar2000a paper do the five constants given by g_hbond correspond?
> >>
> >> The forward and backward rate constant correspond to Eqn. 4.
> >> Relaxation corresponds to the time where C(t) = 1/e
> >> Integral is the integral of C(t)
> >> One way is (I think) the forward rate constant in case the backward is
> >> ignored. According to Luzar the time corresponding to the forward rate
> >> constant should be regarded as "the" hbond lifetime.
> >>
> >>>
> >>> Thanks,
> >>> Isabella
> >>>
> >>> On Wed, 19 Oct 2005, David van der Spoel wrote:
> >>>
> >>>> On Wed, 2005-10-19 at 15:10 +0200, Isabella Daidone wrote:
> >>>>> Hi,
> >>>>>
> >>>>> could you please tell me how the "HB lifetime" that the tool g_hbond
> >>>>> gives
> >>>>> in the output is calculated?
> >>>>> -Is it calculated by a single exponential of the hblife.xvg curve? (if
> >>>>> so
> >>>>> when I fit I don't get the same value :-)
> >>>>> -Is it obtained by direct averaging the mean residence time along the
> >>>>> trajectory?
> >>>> There is a serious error in the version 3.3, it will be corrected in
> >>>> 3.3.1.
> >>>>
> >>>> Lifetime can be computed in different ways, all of which are implemented
> >>>> in g_hbond. Check:
> >>>>
> >>>> @Article{Luzar2000a,
> >>>>  author =       {A. Luzar},
> >>>>  title =        {Resolving the hydrogen bond dynamics conundrum},
> >>>>  journal =      {J. Chem. Phys.},
> >>>>  year =         2000,
> >>>>  volume =       113,
> >>>>  pages =        {10663--10675},
> >>>>  OPTabstract =  {This paper analyzes dynamic properties of hydrogen
> >>>> bonds in liquid water. We use molecular dynamics simulation to calculate
> >>>> different probability densities that govern the time evolution of the
> >>>> formation and rupture of hydrogen bonds. We provide analytical
> >>>> connections between these functions. Excellent agreement with our
> >>>> simulation results is observed. We prove transition state theory rate
> >>>> constant to be identical to the inverse of the associated mean first
> >>>> passage time (hydrogen bond lifetime). Hence, the analysis establishes
> >>>> its Arrhenius temperature dependence. We give the explicit relation
> >>>> between reactive flux correlation function for the relaxation dynamics
> >>>> of hydrogen bonds, and their first passage time probability densities.
> >>>> All the different observations in the existing literature, associated
> >>>> with various estimates of hydrogen bonding times in liquid water that
> >>>> are affected (or not affected) by particular bond criteria, as well as
> >>>> by different definitions of hydrogen bond lifetimes applied in
> >>>> simulation, can be easily reconciled within the framework of reactive
> >>>> flux correlation function approach.},
> >>>>  OPTnote =      {}
> >>>> }
> >>>>>
> >>>>> Thanks
> >>>>> Isabella
> >>>>>
> >>>>> ps. 1) There might be a small error in the  hblife.xvg file. My
> >>>>> trajectory
> >>>>> is sampled every 2 ps and I get in the file: 1,3,5... instead of
> >>>>> 2,4,6...
> >>>>> 2) I'm using the 3.3 version and I get core when I try to use the option
> >>>>> -sel (which I did not get with gromacs 3.1.4)
> >>>>
> >>>> I don't think the -sel option works yet but please file a bugzilla
> >>>> report.
> >>>>
> >>>>> _______________________________________________
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> >>>> --
> >>>> David.
> >>>> ________________________________________________________________________
> >>>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> >>>> Dept. of Cell and Molecular Biology, Uppsala University.
> >>>> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> >>>> phone:  46 18 471 4205          fax: 46 18 511 755
> >>>> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> >>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>>>
> >>>>
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> >> --
> >> David.
> >> ________________________________________________________________________
> >> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> >> Dept. of Cell and Molecular Biology, Uppsala University.
> >> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> >> phone:  46 18 471 4205          fax: 46 18 511 755
> >> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>
> >> _______________________________________________
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> >>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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