[gmx-users] g_hbond in Gromacs-3.2.1

[Ester Chiessi]

>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?
>
>2) What is exactly the meaning of the parameter defined by the option
>-max_h and when should I have to use it?
>
>3) What are the values given in the third column of the file obtained with
>-ac ?
>I supposed the exponential fit of the AC function, but it doesn't seem so
>with my data.
>
>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