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

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 24 23:37:13 CEST 2009

Christopher Rowan wrote:
> Thanks for the response Justin.
> "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 :)"
> I had been using version 3.3.2.
> "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'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."
> Upon switching to version 4.0.2, generation of the index file still
> results in the formation of an empty group; no elements of any of the
> groups containing negative entries.  However, upon running editconf I
> no longer get an error associated with choosing that group, so I
> assume the negative indices have vanished and it was in fact a bug in
> the older version.

That's strange, nevertheless :)  Also, 4.0.2 is still old (2008), and 4.0.5 is 
the latest version.  I have never come across a no-name group being generated in 
any version, however.

> "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."
> It does work without the index file, but I wanted to put all my silver
> atoms in a group so as to be able to freeze them.

You might not need an index group to accomplish this, unless you're only 
choosing a subset of the silver atoms.  Each [ moleculetype ] should be detected 
by grompp from the topology, so as long as you have an AG moleculetype defined, 
then you shouldn't need to specify it in the index.  But then, I don't know the 
entire contents of your system, so this is just conjecture.


> Cheers,
> Chris Rowan
> University of Victoria
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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