[gmx-users] g_hbond gromacs 3.2

Ilya Chorny ichorny at maxwell.compbio.ucsf.edu
Tue Feb 24 00:41:01 CET 2004

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? 
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
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 
comparison. Any help would be greatly appreciated.
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
Tel:  (415)-476-6875                                   600 16th st
Fax:  (415)502-4222                                    San Francisco, CA
Cell: (408)887-8496
                                   Email: ichorny at maxwell.ucsf.edu
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