[gmx-users] g_bond -hx

Ester Chiessi ester.chiessi at uniroma2.it
Mon Mar 5 17:00:56 CET 2007

I used g_hbond with -hx option, to study intramolecular bonding in my 
polymer (a poly(vinyl alcohol) partially hydrophobized with metacrylate 
I found a quite high number of hydrogen bonds between n-n residues. What 
does a HB between n-n residues represent? A intra-residue HB? I have only 8 
residues that could form intra-residue HBs, within a total of 818 residues, 
and I found with g_hbond -hx about 35 n-n HBs per frame. How this result 
could be explained?
I obtained the same results with gromacs 3.2.1 and gromacs 3.3.

Thanks in advance for any suggestion


Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Università di Roma Tor Vergata
Via della Ricerca Scientifica
00133 Roma
tel: *39*6*72594462 

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