[gmx-users] g_hbond

[chris.neale at utoronto.ca]

 From g_hbond -h

"OH and NH groups are regarded as donors, O is an acceptor always, N  
is an acceptor by default, but this can be switched using -nitacc.  
Dummy hydrogen atoms are assumed to be connected to the first  
preceding non-hydrogen atom."

The two groups are to find hbonds between group A and group B. If you  
want to find hbonds within group A, then you specify an index group  
that contains group A two times.

I think that you want:

[ group ]
100 101 200

Then give group 2x as the identical index group.

PS, there were problems with g_hbond a few months ago reported on  
list, I suggest that you check to ensure that these problems were fixed.

Chris.

-- original message --

Hi,
To help clarify my previous g_hbond question, I have these two groups  
in my index file
[ a_100_a_101]      # 100 is N, #101 is H
    100 101
[ a_200 ]                # 200 is O
    200

when I ran g_hbond, I got "Found 1 donors and 2 acceptors". The part  
that I don't quite understand is why it says 2 acceptors. Did I set up  
the groups correctly?

Again, hope this clarifies my question.
Thanks for your insight.

Simon