**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
*

*> 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

**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 ]

*
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 15:57:46 CST
*