Re: Equilibration when splitting an ABF calculation

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Jan 27 2011 - 08:48:48 CST

Dear Jerome,

>Even simpler: you can enable the colvars, including their wall
>potentials, but not ABF (e.g. comment out the abf block).

Aha, so the upper and lower wall potentials are active as soon as a colvar
is defined? That's good to know, thanks.

Best regards,
Ajasja

On Thu, Jan 27, 2011 at 15:08, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:

> Hi Ajasja,
>
> On 27 January 2011 13:25, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
> wrote:
> > Dear all,
> > I partitioned the FES of my system into eight smaller parts. For each
> part I
> > wanted the system to be inside the region of interest (ROI) when
> starting
> > the calculation, so puled the each part to the desired location (using
> the
> > harmonic keyword of the colvars module - fig I). I then slowly relaxed
> > the constraint and let each part equilibrate for a while. For some parts
> the
> > system escaped from the ROI during equlibration (fig II - at least F and
> B
> > are out of ROI). So when the ABF simulation started the system was not
> > inside the boundaries defined for the colvars for some parts.
> > Two questions:
> >
> > Is this a problem? When the ABF started the wall potential will push the
> > system to the right region, but probably with some input of energy.
>
> Indeed, and that defeats the purpose of equilibrating before that...
>
> > How could I have ensured the the system stays in the ROI during
> > equlibration? Should I have ABF turned on during equilibration, but with
> a
> > very high fullsamples, so only the wall potential is active?
>
> Even simpler: you can enable the colvars, including their wall
> potentials, but not ABF (e.g. comment out the abf block).
>
> Cheers,
> Jerome
>

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