# Re: ABF & distanceZ projection axis more

From: HAMID - (h2a1385_at_gmail.com)
Date: Thu Sep 22 2011 - 05:36:32 CDT

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?
>>
>> 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
>>>>
>>>> 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
>>>>>
>>>>> 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
>>>>>
>>>>>
>>>>> ----
>>>>> PhD student of Biophysics,
>>>>> UT, Iran
>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>> ----
>>> PhD student of Biophysics,
>>> UT, Iran
>>>
>>
>>
>> --
>> ----
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