[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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