Re: ABF & distanceZ projection axis

From: Giacomo Fiorin (
Date: Wed Sep 21 2011 - 19:22:36 CDT

Hello Hamid, if you define the distanceZ along the vector (-1, 0, 0) you
will get a certain PMF that has (supposedly) positive and negative values
alike as abscissa.

If you use the vector (1, 0, 0) that will change the sign of x, but not of
the free energy.

That is, the PMF obtained with (-1, 0, 0) should be exactly the same as the
one with (1, 0, 0), just reflected. It's like turning your entire system
around by 180: it won't change the thermodynamics of it.

Of course, you need to be consistent with your chosen boundaries, those need
to change sign in the two alternate configurations.


On Wed, Sep 21, 2011 at 5:15 PM, HAMID - <> wrote:

> Dear all,
> I have a question about distanceZ component of colvar in ABF method. I
> read post about my problem but I did not understand the answer.
> In distanceZ component, the axis (x,y,z) indicates the projection axis
> e of distance (r-r1) vector and the value of such component is
> e.(r-r1). My question is here, does the sign of e vector components
> change the sign of final PMF values?
> In other words, What is the relation between PMF sourced from e vector
> (-1,0,0) and one sourced from e vector (1,0,0)?
> As I inferred from the equation 17-19 of the Henin & Chipot paper
> (JChemPhys, V. 121, N. 7, 2005) If the unit vector is one indicate by
> e vector thus the sign of e component would change the final force.
> Does I inferred correctly?
> I would apologize for disturbing you by such questions. I am looking
> forward for your comments and advices.
> Thanks in advance.
> ----
> H. Hadi
> PhD student of Biophysics,
> UT, Iran

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