**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,
*

*>
*

*> 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.
*

*>
*

*> 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
*

*>> 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
*

*>>
*

*>
*

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

**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 ]

*
This archive was generated by hypermail 2.1.6
: Mon Dec 31 2012 - 23:20:50 CST
*