Re: ABF & distanceZ projection axis more

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Sep 22 2011 - 04:33:02 CDT

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
>

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