[gmx-users] Freeze group atoms changing position

Justin Lemkul jalemkul at vt.edu
Wed Oct 31 21:32:09 CET 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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