Re: Running bias exchange metadynamics simulations with NAMD

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Jan 17 2011 - 08:40:11 CST

Thank you, an interesting reading.
Crude summary for anyone else reading this:
On simple systems both method give similar free energy surfaces (FES).
Metadynamics is designed as a nonequilibrium method, while ABF
uses equilibrium sampling (from the canonical ensemble).
So in simple fast-relaxing systems metadynamics explores the FES more
rapidly, while ABF is more "gentle", but my converge more slowly.
There is also a difference in memory time of the two methods. ABF has
"infinite" memory time, but metadynamics does not (which may or may not be
an advantage).
Lastly metadynamics has currently more colvars avalible in NAMD than ABF.

I have a question (that my be of no importance what so ever):
In figure 4B why are there so many acumulated samples around 9 Angstroms? Is
it because in this region (<12 A) the end to end distance is not a good
colvar anymore?
(and there are also some spikes in 5B)

Best regards,
Ajasja

On Fri, Jan 14, 2011 at 17:37, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:

> On 14 January 2011 16:31, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
> wrote:
> > Dear Giacomo,
> > Thank you for a great explanation!
> > Could I ask another question:
> > What is the difference between metadynamics and ABF? Or more
> specifically,
> > what are the advantages/disadvantages of each method?
>
> Indeed, there are similarities between the two methods. One of the
> goals of this paper:
> http://pubs.acs.org/doi/abs/10.1021/ct9004432
> was to answer your question.
>
> Cheers,
> Jerome
>

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