Re: new NAMD user ABF setup question

From: Giacomo Fiorin (
Date: Thu May 27 2010 - 16:27:02 CDT

Hi Elio, the most intuitive collective variable, or reaction coordinate is
the COM-COM distance, whichever its direction may be. If you want to pull
them apart (and back together!) along a specific direction, you have to
restrict the variable to be on the projection along that "specific
coordinate" as you said: do you mean Cartesian coordinate (x, y or z)? My
suggestion is to use distanceZ from the ABF implementation in NAMD 2.7b1 and
2.7b2, and also define distanceXY with a restraint to be zero, so that
you'll have a straight line, if that's what you want.

The comment you were referring to sounds specific to a well defined system,
which may not be similar to yours. The boundaries defining the relevant
region of your system are your choice entirely.

You should check out the ABF paper and compare it with umbrella sampling
using your own intuition. Too often comparisons between free energy methods
are based on specific examples that may not necessarily be applicable to
your case.

In any case, when the variables are appropriately chosen, ABF DOES give you
an accurate PMF within the range (boundaries) you defined.


---- ----
 Dr. Giacomo Fiorin
 ICMS - Institute for Computational Molecular Science - Temple University
 1900 N 12 th Street, Philadelphia, PA 19122
---- ----

On Thu, May 27, 2010 at 3:10 PM, Elio Cino <> wrote:

> Hello. I have been trying to calculate free energies of peptide binding to
> a protein with umbrella sampling in gromacs with mixed results. Anyways, I
> was hoping the ABF method may help me get accurate results faster than
> umbrella sampling. I have read some of the ABF tutorial and manual, but am a
> bit confused about the ABF setup. I set the boundaries for the COM distance
> between the peptide and protein, but I think I need to specify a direction
> also since I want to pull the peptide away from the protein along a specific
> coordinate. I am unsure if they is correct, and if so how to specify the
> direction. Also, I read a comment saying that much of the ABF calculation
> time is spent climbing uphill to overcome the forces (between peptide and
> protein) at low COM distances and to avoid this, the lower boundary should
> be increased. Will this still provide an accurate PMF? It seems that
> excluding these low boundary states would cause some errors in the delta G.
> Any help is appreciated. Thanks.
> Elio Cino

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