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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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