[gmx-users] g_hbond

[Isabella Daidone]

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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