[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)?
And sorry for asking again,
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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