[gmx-users] g_hbond

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 19 15:48:42 CEST 2005

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

Lifetime can be computed in different ways, all of which are implemented
in g_hbond. Check:

  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

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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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