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

**Date:** Thu Sep 22 2011 - 05:36:32 CDT

**Next message:**Hasan haska: "Re: force question"**Previous message:**Ehsan Ban: "Re: force question"**In reply to:**Jérôme Hénin: "Re: ABF & distanceZ projection axis more"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear Jerome,

Thank you very much for quick reply, I setup a new run in reverse direction.

Best

On 9/22/11, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:

*> Hamid,
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*>
*

*> I would expect the result on graph 3, not graph 2, because the point
*

*> at x=0 must remain the same when you invert the axis.
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*>
*

*> Best,
*

*> Jerome
*

*>
*

*> On 22 September 2011 10:05, HAMID - <h2a1385_at_gmail.com> wrote:
*

*>> Dear Giacomo,
*

*>>
*

*>> I would apologize for disturbing you again.
*

*>> To test my understanding about your response I depict a situation in
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*>> attached pdf file.
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*>> The fig.ABF window shows my setup; a ligand move toward channel lumen
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*>> from bulk water, the first distance along X-axis is about +10 and
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*>> ligand reaches to channel pore at +8.
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*>> Ligand continues its path toward the channel and the distance between
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*>> them be zero when those COM find same position. I set the e vector of
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*>> distanceZ component to (-1,0,0). Final PMF graph is similar to graph
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*>> one. If I change e to (1,0,0) which graphs depict correct results,
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*>> graph 3 or 2?
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*>> I inferred from your previous answer that the graph 2 is correct one.
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*>> Does it correct?
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*>> Thanks in advance for your attentions.
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*>>
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*>> Best.
*

*>>
*

*>>
*

*>> On 9/22/11, HAMID - <h2a1385_at_gmail.com> wrote:
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*>>> Thank you Giacomo!
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*>>> I would be appreciate your clear response.
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*>>>
*

*>>> 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
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*>>>> will get a certain PMF that has (supposedly) positive and negative
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*>>>> values
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*>>>> alike as abscissa.
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*>>>>
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*>>>> If you use the vector (1, 0, 0) that will change the sign of x, but not
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*>>>> of
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*>>>> the free energy.
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*>>>>
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*>>>> That is, the PMF obtained with (-1, 0, 0) should be exactly the same as
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*>>>> the
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*>>>> one with (1, 0, 0), just reflected. It's like turning your entire
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*>>>> system
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*>>>> around by 180°: it won't change the thermodynamics of it.
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*>>>>
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*>>>> Of course, you need to be consistent with your chosen boundaries, those
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*>>>> need
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*>>>> to change sign in the two alternate configurations.
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*>>>>
*

*>>>> Giacomo
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*>>>>
*

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

*>>>>> Dear all,
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*>>>>>
*

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

*>>>>> ----
*

*>>>>> H. Hadi
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*>>>>> PhD student of Biophysics,
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*>>>>> UT, Iran
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*>>>>>
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*>>>>>
*

*>>>>
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*>>>
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*>>>
*

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

*>>>
*

*>>
*

*>>
*

*>> --
*

*>> ----
*

*>> H. Hadi
*

*>> PhD student of Biophysics,
*

*>> UT, Iran
*

*>>
*

*>
*

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

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