[gmx-users] h-bonds in gromacs

Giacomo De Mori demori at icrm.cnr.it
Mon Feb 14 15:25:37 CET 2005

Hi to all
i would like to notice some more problems on g_hbond

1-- on gromacs 3.2.1 the command -hbm (to write the map hbmap.xpm)  doesn't

2 -- on gromacs 3.1.4 this command it works but when i run xpm2ps to convert
in eps files, the index of the hydrogen-bonds are inverted in the eps file,
so, on the top of  the map  (eps) there is the last hydrogen bond instead of
the first, while on the bottom of the map there is the first instead of the
last hydrogen bond. I suppose this is a problem of xpm2ps and not g_hbond.


Attilio wrote:

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