[gmx-users] h-bonds in gromacs

[Attilio]

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

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