Re: turning off fixed atoms in the middle of simulation

From: Jim Phillips (
Date: Wed Dec 15 2004 - 11:15:47 CST


You need to specify "fixedAtomsForces on" in your initial configuration
(back where you originally have "fixedAtoms on"). NAMD normally would
skip interactions between fixed atoms, which improves performance if you
have a large number of them. Using "fixedAtomsForces on" causes these
interactions to be calculated, so that "fixedAtoms off" just has to
disable the code in the integrator that keeps fixed atoms from moving.


On Wed, 15 Dec 2004, Vani Krishna wrote:

> Dear NAMD users:
> Is there a way i can turn off fixed atoms in the
> middle of a run? that is if i want to fix certain
> atoms for 300 ps and then release them and do
> minimization and then regular MD, how should my script
> be?
> I tried the following but didn't work:
> fixedAtoms off
> minimize 1000
> reinitvels $temperature
> run 300000
> ----------
> is there any way to do this?
> Thanks
> Vani
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