[gmx-users] Hydrogen Bond Lifetime

[David van der Spoel]

Laercio Pol Fachin wrote:
> Hi, all.
> 
> I am analyzing the hydrogen bond lifetime of water molecules around 
> polar atoms of my molecule. However, I have faced different HB lifetime 
> definitions in different sources. A sample of what I obtained employing 
> g_hbond is below:
> 
> "g_hbond -f .xtc -s .tpr -n .ndx -ac .xvg -b 0 -e 10000"
> 
> Type      Rate (1/ps)  Time (ps)  DG (kJ/mol)
> Forward         0.797      1.254       5.089
> Backward        0.061     16.475      11.474
> One-way         1.323      0.756       3.835
> Integral        0.948      1.055       4.661
> Relaxation      2.195      0.456       2.579
> 
> # In GROMACS 3.3 manual, page 171, it is said that "the integral of C(t) 
> gives a rough estimate of the average H-bond lifetime", which points to 
> a HB lifetime of 1.055 ps (right?);
> # On the other hand, in previous discussion in this list, I have found 
> that "according to Luzar the time corresponding to the forward rate 
> constant should be regarded as 'the' hbond lifetime", which points to a 
> HB lifetime of 0.797;
> 
> Can anyone please clarify such points?
@Article{ Luzar2000a,
   author =       "A. Luzar",
   title =        "Resolving the hydrogen bond dynamics conundrum",
   journal =      BTjcp,
   year =         2000,
   volume =       113,
   pages =        "10663--10675",
}
@Article{ Spoel2006b,
   author =       "D. {van der Spoel} and P. J. {van Maaren} and
                   P. Larsson and N. T{\^i}mneanu",
   title =        "Thermodynamics of hydrogen bonding in hydrophilic
                   and hydrophobic media",
   journal =      BTjpcb,
   year =         2006,
   volume =       110,
   pages =        "4393-4398"
}



> 
> Thanks in advance,
> Laércio Pol-Fachin
> 
> 
> ------------------------------------------------------------------------
> Novos endereços, o Yahoo! que você conhece. Crie um email novo 
> <http://br.rd.yahoo.com/mail/taglines/mail/*http://br.new.mail.yahoo.com/addresses> 
> com a sua cara @ymail.com ou @rocketmail.com.
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
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://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++