[gmx-users] Measuring Atom Distances

Javad Azadi jazadi at chemistry.ohio-state.edu
Tue Jul 4 07:24:19 CEST 2006

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?


"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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