[gmx-users] g_hbond, residue selection and boundary conditions

Nicolas nsapay at ucalgary.ca
Thu Oct 2 01:27:18 CEST 2008

Hello everybody,

I want to track the number of hydrogen bonds between a lipid and the 
rest of my system. It is quite strait forward to do with g_hbond. I've 
got few questions though:

    1. Does g_hbond takes into account the periodic boundary conditions
    or should first I center the system on my molecule, then run g_hbond?

    2. When I run g_hbond, it prints the message "No option -sel" the
    usual welcome message and run normally after that. I don't use any
    -sel option in the command line. Is it because I'm using g_hbond
    from gmx 3.3.3 with a trajectory from gmx 3.3.1? I use the following
    command line:

        g_hbond -f part03.xtc -s part03.tpr -n index.ndx -num part03.xvg

    3. When g_hbond ask for 2 groups, is it the same think to specify
    group1 then group2 and group2 then group1? (assuming group1 and
    group2 do not overlap)

Thanks in advance for you answer,

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