Equilibration when splitting an ABF calculation

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Jan 27 2011 - 06:25:04 CST

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<http://img577.imageshack.us/img577/3500/abfroi.jpg>).
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 - <http://img62.imageshack.us/img62/5697/abfroiequ.jpg> 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.
   - 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?

Best regards,
Ajasja Ljubetič
Young reasercher,
Laboratory of biophysics,
Institute Jožef Štefan,
Ljubljana, Slovenia

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