On 10/31/12 4:21 PM, Christopher Neale wrote:
Well, I thought that it would work for for freeze groups, and that is what I
intended to say. I've used freeze groups
before, but don't have tonnes of experience with them. The gromacs mdp options
page reads as if it should work (
http://manual.gromacs.org/online/mdp_opt.html#neq ), but if Justin says that
you can not use an index group for freeze groups (only position restraints)
then I suggest that you take his word for it. He answers a lot more posts and
is probably more familiar with the ins and outs of gromacs.
That's not what I meant at all. One can use an index group for freeze groups,
as well. The original problem was that apparently the frozen group was not
working entirely, so I suggested (as a troubleshooting measure) that the OP use
restraints instead to see if the outcome was different. The bizarre behavior
before (two molecules moving, but the remainder staying frozen) suggested to me
that perhaps there was something going wrong with the initial configuration and
I was hoping that, at the very least, using restraints would determine if the
configuration was messed up or not amenable to freezing.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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