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

Christopher Rowan chriskrowan at gmail.com
Wed Jun 24 20:50:38 CEST 2009

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.

"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

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.

Chris Rowan
University of Victoria

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