[gmx-users] Measuring Atom Distances

[Marcos Villarreal]

If after using g_dist correctly you still get 0 (or nan) distances, one of 
your atoms have 0 mass (like N in NH3 with virtual sites). In that case you 
could make a temporary tpr to feed g_dist with non cero mass by manually 
editing the .top

Saludos,
		Marcos

On Tuesday 04 July 2006 07:40, Tsjerk Wassenaar wrote:
> Hi Javad,
>
> You don't need to bother using make_ndx, just create a file atoms.ndx
> which reads like this:
>
> [ atom1 ]
> number_of _first_atom
> [ atom2 ]
> number_of_second_atom
>
> Cheers,
>
> Tsjerk
>
> On 7/4/06, Javad Azadi <jazadi at chemistry.ohio-state.edu> wrote:
> > Is it just a matter of using make_ndx -f traj.gro
> >
> > >a (atom1 number from .gro) (atom2 number from .gro)
> >
> > then selecting keep # where # is the index just created?
> >
> > Javad
> >
> > "Dallas B. Warren" <Dallas.Warren at vcp.monash.edu.au> said:
> > > > I tried g_dist, and the out put is nothing but zeros.  I only
> > > > have the two unconnected atoms indexed that I want to
> > > > measure, could that be the problem?
> > >
> > > I would check what you are doing.  It shouldn't matter whether the
> > > atoms are connected or not, g_dist will measure the distance between
> > > them. Are you sure you have set up the index groups correctly?
> > >
> > > Catch ya,
> > >
> > > Dr. Dallas Warren
> > > Lecturer
> > > Department of Pharmaceutical Biology and Pharmacology
> > > Victorian College of Pharmacy, Monash University
> > > 381 Royal Parade, Parkville VIC 3010
> > > dallas.warren at vcp.monash.edu.au
> > > +61 3 9903 9524
> > > ---------------------------------
> > > When the only tool you own is a hammer, every problem begins to
> > > resemble a nail.
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-- 
Grupo de Biofísica
CIQUIBIC-Dpto Química Biológica
Facultad de Ciencias Químicas
Universidad Nacional de Córdoba
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