Re: problem with minimization and calculation of force on a fixed atom

From: Jérôme Hénin (
Date: Thu Aug 31 2017 - 17:36:54 CDT

I've been told of a certain command named fixedAtomsForces that sounds just
like what you need :-)


On 1 September 2017 at 00:03, Ben Adams <> wrote:

> Dear NAMD users,
> I want to calculate forces on a few constrained atoms while I'm doing
> merely energy minimization. I used colvars with harmonic restraints and
> obtained force based on the distance of the atom of interest to a specified
> Center value. But the minimization causes dramatic fluctuations on
> calculation of force. Changing the force constant, minimization options
> mentioned in tutorial don't help that much. and the results are not even
> reproducible.
> An alternative way would be to freeze that atom and calculate the force
> directly. But using the 'fixedAtoms' option leaves the force at the atom
> equal to zero and do not allow to extract its value.
> Is there any other way to freeze an atom while the force on it is being
> calculated?
> Or is there anyway to make minimization more stable when a colvar
> constraint is present?
> Thanks in advance,

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