[gmx-users] Measuring Atom Distances

[Javad Azadi]

Tsjerk,

This time I had the output I desired, but when comparing it to the same output from VMD, there are 
discrepancies at every step.  They're about 5A off from each other.  I believe it has to do with how 
they measure the distance.  In VMD, it would seem it understands the desired molecule can go so far 
out of the box and still be whole; while in GMX, it takes it as two atoms of two different molecules.  
How can I make sure that g_dist measures the distance for one molecule?  Does it involve using a 
command during trjconv?

Thanks,
Javad 
Undergraduate Researcher
The Ohio State University
jazadi at chemistry.osu.edu

Tsjerk Wassenaar <tsjerkw at gmail.com> said:

> 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.
> > > _______________________________________________
> > > 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.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> >
> >
> >
> > --
> >
> >
> >
> > _______________________________________________
> > 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.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> 
> 
> -- 
> 
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336
> _______________________________________________
> 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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 



--