[gmx-users] g_hbond in Gromacs-3.2.1

[David van der Spoel]

On Mon, 2004-10-18 at 14:09, Ester Chiessi wrote:
> >Dear all
> >
> >I'd have some questions about g_hbond in Gromacs-3.2.1. I'm using this tool
> >with trajectories already examinated with g_hbond in Gromacs-2.1.4.
> >
> 
> Sorry. I typed 2 instead of 3. The version was 3.1.4, not 2.1.4.
> 
> 
> >1) Why does the AC function become negative at high times?
There are two curves in your output file, the first one is scaled to go
to zero at large time, the second is the original one.
> >
> >2) What is exactly the meaning of the parameter defined by the option
> >-max_h and when should I have to use it?
Normally you don't need it. I've put it in but never used it.
> >
> >3) What are the values given in the third column of the file obtained with
> >-ac ?
See above.

> >I supposed the exponential fit of the AC function, but it doesn't seem so
> >with my data.
That's correct:
@Article{Luzar96b,
  author =       {A. Luzar and D. Chandler},
  title =        {Hydrogen-bond kinetics in liquid water},
  journal =      BTnature,
  year =         1996,
  volume =       379,
  pages =        {55-57}
}
 

> >
> >I tried to use the option -shell with -dan, but the file defined in -dan
> >was not written, though it was reported in the output of g_hbond. (In the
> >preceeding Gromacs version I used -da with no problem).
> >
> >Thanks in advance for any help.
> >
> >Ester
> >
> >Ester Chiessi
> >Dipartimento di Scienze e Tecnologie Chimiche
> >Università di Roma Tor Vergata
> >Via della Ricerca Scientifica
> >00133 Roma
> >tel. +39 06 72594462
> >fax  +39 06 72594328
> >http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
> >
> >
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> 
> 
> Ester Chiessi
> Dipartimento di Scienze e Tecnologie Chimiche
> Università di Roma Tor Vergata
> Via della Ricerca Scientifica
> 00133 Roma
> tel. +39 06 72594462
> fax  +39 06 72594328
> http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
> 
> 
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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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