[gmx-users] WARNING: negative index -1 in group System

[Justin A. Lemkul]

Christopher Rowan wrote:
> Hi,
> 
> Allow me to be the first to archive a message with "negative index".
> 
> I ask for an index file:
> make_ndx_s -f ???.pdb -o ???.ndx
> and specify:
> a AG
> to select all the silver atoms into a group.
> The index file then clearly numbers and lists the atoms: all in [
> system ], again all atom numbers in empty brackets [   ] and then my
> silver atoms in the [ AG ] group.

First, it would be helpful to know which version of Gromacs you're using, 
especially if this is a bug in an older version.  If it is the most current 
version (4.0.5), it is of much greater interest :)

What I don't understand is why you have a group with no name; that shouldn't be. 
  If you're defining AG atoms, then you should have [ System ] and [ AG ].

> I proceed to define a box:
> editconf_s -f ???.pdb  -n ???.ndx -o ???.gro -bt cubic
> 
> The output gives:
> 
> ...
> Select a group for output:
> 
> WARNING: negative index -1 in group System
> 

I'm assuming you've check the entire [ System ] directive to ensure that all 
indices are positive?  With the generation of a "no-name" group, it is possible 
that something funky is going on.

> 
> WARNING: negative index -1 in group System
> 
> Group     0 (      System) has    68 elements
> Group     1 (          AG) has    13 elements
> Select a group: 0
> Selected 0: 'System'
> Segmentation fault
> 

Does the command work without the index file?  If you're specifying a box to 
contain the entire system, then you shouldn't need the index file.

-Justin

> Perplexing.
> 
> I found Travis Trudeau's message about having a zero index and tried
> finding atom numbering:
> grompp_s -f ???.mdp -c ???.pdb -p ???.top -o ???.tpr -n ???.ndx
> 
> But again got:
> 
> ...
> initialising group options...
> processing index file...
> 
> WARNING: negative index -1 in group System
> 
> 
> WARNING: negative index -1 in group System
> 
> Making dummy/rest group for T-Coupling containing 33 elements
> ...
> 
> So, if anyone could shed some light on how to overcome the negative
> index hurdle it would be much appreciated,
> Chris Rowan
> University of Victoria
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> 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
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================