Re: [gmx-users] Hydrogen Bond Lifetime

2008-10-02 Thread Omer Markovitch 
Please see also my reply under HB lifetime to Christopher Daub.
I think that JCP 129, 84505 (2008) should be read when dealing with C(t) in
general  HB lifetimes in particular.
** link: http://dx.doi.org/10.1063/1.2968608

Omer Markovitch.
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[gmx-users] Hydrogen Bond Lifetime

2008-09-30 Thread Laercio Pol Fachin 
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 1

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?

Thanks in advance,
Laércio Pol-Fachin



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Re: [gmx-users] Hydrogen Bond Lifetime

2008-09-30 Thread 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 1

Type  Rate (1/ps)  Time (ps)  DG (kJ/mol)
Forward 0.797  1.254   5.089
Backward0.061 16.475  11.474
One-way 1.323  0.756   3.835
Integral0.948  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



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--
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
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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