From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
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 :-)
Jerome
On 1 September 2017 at 00:03, Ben Adams <benny.adams1993_at_gmail.com> 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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