Re: Running bias exchange metadynamics simulations with NAMD

From: Ajasja Ljubetič (
Date: Fri Jan 14 2011 - 09:31:49 CST

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?

I know that in metadynamics one adds N-dimentional gaussian "hills"
according to where the system is located currently. The free energy surface
(FES) is then approximatively opposite to the sum of the hills once the
trajectory has converged (ie the system is moving in a diffusive manner).

And in ABF the FES is obtained by integrating the free energy gradient. The
gradient is opposite to the average force at a particular value of a colvar.
This force is sampled during a number of steps (in NAMD set by *fullSamples)
But why is one approach better than the other? By adding a hill in
metadynamics you basically add a force as well (isn't the force the negative
gradient of the hill potential?)

Thank you & best regards,

On Tue, Jan 4, 2011 at 01:13, Giacomo Fiorin <>wrote:

> Hi Asjasja, the difference is the following:

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