[gmx-users] Measuring Atom Distances
Alessandro at polymer.kth.se
Tue Jul 4 12:02:25 CEST 2006
let's say that I have two subset of atoms, let's call them i, j, k (first group A) and l, m, n (second group B).
Is there any elegant way (rather than iterating g_dist) of having the average over the trajectory and over ALL the possible permutation over the two subset A and B.
M.Phil., Ph.D. student
Dept. of Fibre and Polymer Technology
Royal Institute of Technology
From: gmx-users-bounces at gromacs.org on behalf of Tsjerk Wassenaar
Sent: Tue 7/4/2006 9:40 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Measuring Atom Distances
You don't need to bother using make_ndx, just create a file atoms.ndx
which reads like this:
[ atom1 ]
[ atom2 ]
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?
> "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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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
9747AG Groningen, The Netherlands
+31 50 363 4336
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