From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Jan 17 2011 - 10:35:20 CST
On 17 January 2011 15:40, Ajasja LjubetiÄ <ajasja.ljubetic_at_gmail.com> wrote:
> Thank you, an interesting reading.
> CrudeÂ summary for anyone else reading this:
> On simple systems both method give similar free energy surfaces (FES).
> Metadynamics is designed as a nonequilibriumÂ method, while ABF
> usesÂ equilibriumÂ sampling (from the canonicalÂ ensemble).
> So in simple fast-relaxing systems metadynamics explores the FES more
> rapidly, while ABF is more "gentle", but my converge moreÂ slowly.
> There is also a difference in memory time of the two methods. ABF has
> "infinite" memory time, but Â metadynamics does not (which may or may not be
> an advantage).
> LastlyÂ metadynamicsÂ has currently more colvars avalible in NAMD than ABF.
Thanks for the summary!
> I have a question (that my be of no importance what so ever):
> In figure 4B why are there so many accumulated samples around 9Â Angstroms? Is
> it because in thisÂ region (<12 A) the end to end distance is not a good
> colvar anymore? (and there are also some spikes in 5B)
That's right. The conformational space is more complex there, so the
1D (and even 2D) descriptions are ambiguous: one value of these
coordinates corresponds to several, completely different
conformations. The adaptive bias then converges very slowly and the
system gets "stuck" at these locations.
> On Fri, Jan 14, 2011 at 17:37, JÃ©rÃ´me HÃ©nin <jhenin_at_ifr88.cnrs-mrs.fr>
>> On 14 January 2011 16:31, Ajasja LjubetiÄ <ajasja.ljubetic_at_gmail.com>
>> > DearÂ Giacomo,
>> > Thank you for a great explanation!
>> > Could I ask another question:
>> > What is the difference betweenÂ metadynamicsÂ and ABF? Or more
>> > specifically,
>> > what are theÂ advantages/disadvantages of each method?
>> Indeed, there are similarities between the two methods. One of the
>> goals of this paper:
>> was to answer your question.
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