**From:** Jérôme Hénin (*jhenin_at_ifr88.cnrs-mrs.fr*)

**Date:** Thu Sep 22 2011 - 04:33:02 CDT

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

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
*

*>
*

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

*
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 15:57:46 CST
*