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<P><FONT SIZE=2>Hi all<BR>
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).<BR>
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.<BR>
Thanx<BR>
Regards<BR>
<BR>
Alessandro Mattozzi<BR>
M.Phil., Ph.D. student<BR>
Dept. of Fibre and Polymer Technology<BR>
Royal Institute of Technology<BR>
Stockholm, Sweden<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: gmx-users-bounces@gromacs.org on behalf of Tsjerk Wassenaar<BR>
Sent: Tue 7/4/2006 9:40 AM<BR>
To: Discussion list for GROMACS users<BR>
Subject: Re: [gmx-users] Measuring Atom Distances<BR>
<BR>
Hi Javad,<BR>
<BR>
You don't need to bother using make_ndx, just create a file atoms.ndx<BR>
which reads like this:<BR>
<BR>
[ atom1 ]<BR>
number_of _first_atom<BR>
[ atom2 ]<BR>
number_of_second_atom<BR>
<BR>
Cheers,<BR>
<BR>
Tsjerk<BR>
<BR>
On 7/4/06, Javad Azadi <jazadi@chemistry.ohio-state.edu> wrote:<BR>
> Is it just a matter of using make_ndx -f traj.gro<BR>
><BR>
> >a (atom1 number from .gro) (atom2 number from .gro)<BR>
><BR>
> then selecting keep # where # is the index just created?<BR>
><BR>
> Javad<BR>
><BR>
> "Dallas B. Warren" <Dallas.Warren@vcp.monash.edu.au> said:<BR>
><BR>
> > > I tried g_dist, and the out put is nothing but zeros. I only<BR>
> > > have the two unconnected atoms indexed that I want to<BR>
> > > measure, could that be the problem?<BR>
> ><BR>
> > I would check what you are doing. It shouldn't matter whether the atoms<BR>
> > are connected or not, g_dist will measure the distance between them.<BR>
> > Are you sure you have set up the index groups correctly?<BR>
> ><BR>
> > Catch ya,<BR>
> ><BR>
> > Dr. Dallas Warren<BR>
> > Lecturer<BR>
> > Department of Pharmaceutical Biology and Pharmacology<BR>
> > Victorian College of Pharmacy, Monash University<BR>
> > 381 Royal Parade, Parkville VIC 3010<BR>
> > dallas.warren@vcp.monash.edu.au<BR>
> > +61 3 9903 9524<BR>
> > ---------------------------------<BR>
> > When the only tool you own is a hammer, every problem begins to resemble<BR>
> > a nail.<BR>
> > _______________________________________________<BR>
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><BR>
><BR>
><BR>
> --<BR>
><BR>
><BR>
><BR>
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<BR>
<BR>
--<BR>
<BR>
Tsjerk A. Wassenaar, M.Sc.<BR>
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<BR>
Dept. of Biophysical Chemistry<BR>
University of Groningen<BR>
Nijenborgh 4<BR>
9747AG Groningen, The Netherlands<BR>
+31 50 363 4336<BR>
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