# [gmx-users] g_hbond

Isabella Daidone i.daidone at caspur.it
Thu Nov 3 18:40:23 CET 2005

```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)?

which is the equation in Luzar's article corresponding to the One-way
life time of HB?

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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