[gmx-users] h-bonds in gromacs
Giacomo De Mori
demori at icrm.cnr.it
Mon Feb 14 17:15:02 CET 2005
Giacomo De Mori wrote:
> 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.
opss... sorry this second is not a bug, i misunderstood while i was reading the
xpm files with a text editor
> 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
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users