From: HAMID - (h2a1385_at_gmail.com)
Date: Thu Sep 22 2011 - 03:05:07 CDT
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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