**From:** HAMID - (*h2a1385_at_gmail.com*)

**Date:** Thu Sep 22 2011 - 01:20:02 CDT

**Next message:**Namd Namd: "save the last frame as a pdb file using dcd file"**Previous message:**Axel Kohlmeyer: "Re: Quick TCl scripting question"**In reply to:**Giacomo Fiorin: "Re: ABF & distanceZ projection axis"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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
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*> will get a certain PMF that has (supposedly) positive and negative values
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*> alike as abscissa.
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*>
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*> If you use the vector (1, 0, 0) that will change the sign of x, but not of
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*> the free energy.
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*>
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*> That is, the PMF obtained with (-1, 0, 0) should be exactly the same as the
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*> one with (1, 0, 0), just reflected. It's like turning your entire system
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*> around by 180°: it won't change the thermodynamics of it.
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*>
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*> Of course, you need to be consistent with your chosen boundaries, those need
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*> to change sign in the two alternate configurations.
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*>
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*> Giacomo
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*>
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*> On Wed, Sep 21, 2011 at 5:15 PM, HAMID - <h2a1385_at_gmail.com> wrote:
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*>
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*>> Dear all,
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*>>
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*>> I have a question about distanceZ component of colvar in ABF method. I
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*>> read post about my problem but I did not understand the answer.
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*>>
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*>> In distanceZ component, the axis (x,y,z) indicates the projection axis
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*>> e of distance (r-r1) vector and the value of such component is
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*>> e.(r-r1). My question is here, does the sign of e vector components
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*>> change the sign of final PMF values?
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*>> In other words, What is the relation between PMF sourced from e vector
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*>> (-1,0,0) and one sourced from e vector (1,0,0)?
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*>> As I inferred from the equation 17-19 of the Henin & Chipot paper
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*>> (JChemPhys, V. 121, N. 7, 2005) If the unit vector is one indicate by
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*>> e vector thus the sign of e component would change the final force.
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*>> Does I inferred correctly?
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*>>
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*>> I would apologize for disturbing you by such questions. I am looking
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*>> forward for your comments and advices.
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*>>
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*>> Thanks in advance.
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*>>
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*>> ----
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*>> H. Hadi
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*>> PhD student of Biophysics,
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*>> UT, Iran
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*>>
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*>>
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*>
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-- ---- H. Hadi PhD student of Biophysics, UT, Iran

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