Re: ABF & distanceZ projection axis

From: HAMID - (h2a1385_at_gmail.com)
Date: Thu Sep 22 2011 - 01:20:02 CDT

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

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