From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Jan 27 2011 - 08:08:12 CST
On 27 January 2011 13:25, Ajasja LjubetiÄ <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)Â Â when starting
> the calculation, so puled the each part to the desired location (using the
> harmonic keyword of the colvars module - fig I). I thenÂ slowlyÂ relaxed
> theÂ constraintÂ and let each partÂ equilibrateÂ 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 theÂ 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).
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