VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 16 2008 - 01:33:59 CDT

Hi,
  VMD allows the use of both zero-based and one-based indexing,
depending on whether you use the atom selection keyword "index"
or "serial". When comparing selections between programs you
should always verify that you're using the same indexing scheme,
as there are natural variations between programming languages,
file formats, and many other source that can confound one's assumptions
of data portability between different software packages.

Cheers,
  John

On Fri, May 16, 2008 at 11:08:22AM +0500, Alexandre A. Vakhrouchev wrote:
> Thank you John!
> That was the solution I was thinking of. BTW, why VMD and NAMD atom
> indexing differs? First starts with "0" and the second from "1"? Is it
> an "egg war"?))) I ask because recently have made huge simulation
> pushing wrong atom)
>
> 2008/5/16 John Stone <johns_at_ks.uiuc.edu>:
> >
> > Hi,
> > If I correctly interpret your question, it would seem that you
> > want to load and display a reduced trajectory, along with a full system?
> > If that's what you want to do, the easiest way to do this would be to
> > load them into two independent molecules in VMD. You would then
> > be able to display the full system as well as animate the reduced
> > trajectory at the same time.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
>
> --
> Best regards,
>
> Dr. Alexander Vakhrushev
> Institute of Applied Mechanics
> Dep. of Mech. and Phys.-Chem.
> of heterogeneous mediums
> UB of Russian Academy of Sciences
> 34 T. Baramzinoy St.
> Izhevsk, Russia 426067 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078