[gmx-users] Freeze group atoms changing position

Christopher Neale chris.neale at mail.utoronto.ca
Wed Oct 31 21:21:36 CET 2012

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.


-- original message --

Alex Marshall amarsh59 at uwo.ca 
Wed Oct 31 20:55:08 CET 2012
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Chris, is that for freeze groups or position restraints?

On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale <
chris.neale at mail.utoronto.ca> wrote:

> No need to rename... just make an .ndx group.
> -- original message --
> As I understand it, position restraints for an atom are set in the topology
> file and applied to that atom in each of that species. In order to restrain
> some but not all of the water I'd have to copy the topology of my water
> model and add the restraints, then rename (and group together) the atoms I
> want to freeze so that they're identified with the appropriate topology
> file. Does this sound like it would work? Is there some other way that you
> might do it?
> Thanks

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