[gmx-users] position restraints

David Mobley dmobley at gmail.com
Thu Dec 29 18:53:23 CET 2005

I think you can freeze some atoms using freeze groups, but I haven't
used this myself. With regards to time-dependent restraints, I haven't
done this either, and generally tend to think that doing anything in a
time-dependent way is bad, as it's difficult to be sure you're doing
it slowly enough that it has time to equilibrate at each restraint
potential. How important this is depends somewhat on what exactly you
are trying to do, though. I guess if you are just trying to set up
your system with initial restraints and then gradually turn them off
it makes some sense. Someone else may know if this is possible; I
can't think of a way right now. Alternatively you could run a series
of shorter simulations one after another, with gradually diminishing
restraint potentials.

On 12/29/05, Michal Kolinski <mkolin at iimcb.gov.pl> wrote:
> Hi all
> 1)I have a short question.  Is there a way to slowly release position
> restraints during MD.
> (for example:  force from 1000 to 10,  during 100ps simulation).
> 2) How can I freeze some atoms during EM (atoms move slightly when I
> use very large force for position restraints) ?
> Than you for help.
> Michal
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