[gmx-users] g_hbond gromacs 3.2

David spoel at xray.bmc.uu.se
Tue Feb 24 08:27:01 CET 2004


On Tue, 2004-02-24 at 00:39, Ilya Chorny wrote:
> Hi david,
> 
>  
> 
> I have a couple questions about g_hbond. I noticed an Oct 2003  post
> where you mention completely rewriting g_hbond.
> 
>  
> 
> Is the second column in the –ac output a fit to the first column? 
> 
The first column is corrected for a finite system, i.e. the C(t) does
not go to zero, the second column is the raw C(t)
>  
> 
> Also I noticed that when I use –noda and reduce the –r  value to .25
> it doesn’t work. 
> 
> It gives me the same output as if I didn’t use the –noda option. I
> then compared my results using g_hbond_3.1.4 (r .25) and g_hbond (r
> .35) and got 
> 
> very different results. The version 3.2 C(t) decays slower. My system
> is a solute in  a box of solvent molecules. Since I can’t use the
> –noda option I can’t make a direct 
> 
It decays slower because by default hbonds with different H (e.g.
between two water molecules there are four possible Hbonds) are merged.
This you can turn off with -nomerge.

FInally, I'm still busy rewriting parts of the code since hbonds between
two groups did not work anymore.


> comparison. Any help would be greatly appreciated.
> 
>  
> 
> Thanks
> 
>  
> 
> Ilya
> 
>  
> 
>  
> 
> 3.1.4       g_hbond –r .25 –shell 1.0 -ac
> 
> 3.2       g_hbond  -r.35  -shell 1.0 -ac
> 
>  
> 
>  
> 
>  
> 
>             
> 
> ----------------------------------------------------------------------------------------------
> 
> Dr. Ilya Chorny                                           Department
> of Pharmaceutical Chemistry
> 
> DOE/SLOAN Postdoctoral Researcher       University of California, San
> Francisco
> 
> Tel: (415)-476-6875                                  600 16th st
> 
> Fax: (415)502-4222                                   San Francisco, CA
> 94107
> 
> Cell: (408)887-8496
> 
>                                   Email: ichorny at maxwell.ucsf.edu
> 
> ----------------------------------------------------------------------------------------------
> 
>  
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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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