**From:** HAMID - (*h2a1385_at_gmail.com*)

**Date:** Thu Sep 22 2011 - 03:05:07 CDT

**Next message:**HAMID -: "Re: save the last frame as a pdb file using dcd file"**Previous message:**Hasan haska: "force question"**Next in thread:**Jérôme Hénin: "Re: ABF & distanceZ projection axis more"**Reply:**Jérôme Hénin: "Re: ABF & distanceZ projection axis more"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear Giacomo,

I would apologize for disturbing you again.

To test my understanding about your response I depict a situation in

attached pdf file.

The fig.ABF window shows my setup; a ligand move toward channel lumen

from bulk water, the first distance along X-axis is about +10 and

ligand reaches to channel pore at +8.

Ligand continues its path toward the channel and the distance between

them be zero when those COM find same position. I set the e vector of

distanceZ component to (-1,0,0). Final PMF graph is similar to graph

one. If I change e to (1,0,0) which graphs depict correct results,

graph 3 or 2?

I inferred from your previous answer that the graph 2 is correct one.

Does it correct?

Thanks in advance for your attentions.

Best.

On 9/22/11, HAMID - <h2a1385_at_gmail.com> wrote:

*> Thank you Giacomo!
*

*> I would be appreciate your clear response.
*

*>
*

*> Best
*

*>
*

*> On 9/22/11, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:
*

*>> 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.
*

*>>
*

*>> Giacomo
*

*>>
*

*>> On Wed, Sep 21, 2011 at 5:15 PM, HAMID - <h2a1385_at_gmail.com> 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
*

*>>>
*

*>>>
*

*>>
*

*>
*

*>
*

*> --
*

*> ----
*

*> H. Hadi
*

*> PhD student of Biophysics,
*

*> UT, Iran
*

*>
*

-- ---- H. Hadi PhD student of Biophysics, UT, Iran

- application/pdf attachment: ABFpic.pdf

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