[gmx-users] g_hbond

[David]

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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