From: Jovan Dragelj (jovandragelj_at_gmail.com)
Date: Fri Nov 29 2019 - 12:36:07 CST
Thank you for a very helpful answer!
I assumed this about "constraints" (or maybe soon to be
"positionRestraints") and it's very good to know how it truly works.
I will continue my trials with "extraBonds", following the suggestions with
constants. Reasonable rigidity is the goal, just to bridge the fact that
there are no parameters.
On Fri, Nov 29, 2019 at 12:19 PM Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> Hi Jovan,
> 1) NAMD doesn't have the kind of constraint algorithms that would make
> this cluster literally rigid. (I'm still waiting for the "constraints"
> option to be renamed "positionRestraints", I might just publish a NAMD fork
> that only does that as a form of protest.*)
> 2) you can achieve a physically correct result (reasonable rigidity, as
> you said) using harmonic restraints, and then extrabonds is probably the
> most convenient way.
> 3) then all you need is a trade-off between rigidity and stability of the
> simulation. If you go much higher than the usual force constants for bonded
> terms in the force fields, then you'll need to reduce your integration
> timestep accordingly. So you'll need to ask yourself how much fluctuation
> you can tolerate. My guess is, typical bonded force constants will give
> fluctuations that are physically acceptable, given the level of
> approximation of the force field overall.
> * Too bad that this would break everyone's workflow, including CHARMM-GUI--000000000000f79cb80598808281--
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