[gmx-users] h-bonds in gromacs

Attilio vargiu at sissa.it
Mon Feb 14 10:10:03 CET 2005

Hi all,
I have a stupid question on the calculation of h bonds in gromacs.
I read that probably there is a bug in the code (in particular I'm
pretty sure that is this the case when I tried to use the -sel
option...), then I wrote a small program that calculate h-bonds between
3 atoms (donor-hydrogen-acceptor) using distances between donor and
acceptor, and the angle donor-hydrogen-acceptor. I used cutoffs of 0.35
nm and 30° from a plate angle. Distances and angles are calculate
respectively by g_dist and g_angle.
Now, I didn't put any constraint on the time the hbond have to exist, I
mean that also an h-bond that survive only 1 step is for my an h-bond
(I'm using a time step of 1.5 fs, saving trajectory each 1000 steps).
I observed that results from my program are very different from those of
g_hbond, and in particular the strange thing is that g_hbond calculate
the existence of hbonds more frequently that my program, that is
unespected for my...
Could you somebody explain me why? Which result I must trust? I was
thinking until today that g_hbond calculates bonds only applying
conditions on distance and angles, but now I'm not more sure of this.

Many thanks in advance,

Attilio Vargiu, PhD at SISSA, Trieste (Italy), office number 00390403787302

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