**From:** Jérôme Hénin (*jerome.henin_at_ibpc.fr*)

**Date:** Thu Jun 20 2013 - 16:18:57 CDT

**Next message:**Jeffrey Potoff: "Re: Insertion of GPCR in the POPC Bilayer"**Previous message:**Aron Broom: "Re: Insertion of GPCR in the POPC Bilayer"**In reply to:**Kasra Fattah: "Free Energy Calculation Question"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi Kasra,

To get the y PMF you need to integrate over the x variable:

pmf(y) = - RT * ln (sum_x ( exp(-beta * pmf(x , y) )))

Cheers,

Jerome

----- Original Message -----

*>
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*> Hi all,
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*>
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*>
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*> I'm calculation the pmf of a system using ABF method. One I did it
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*> for a 1D collective variable that is the distanceZ of a molecule
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*> from a specific point along y-direction. Next I'm doing a 2d pmf
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*> calculation using the collective variable along both x and y
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*> direction and I get a surface of pmf. Now to test if the results
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*> from 2d are consistent with my 1d results:
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*>
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*>
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*> Is the following procedure right?
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*>
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*>
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*> I average the results while keeping one of the reaction coordinates
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*> constant (eg. at a constant y) with respect to the Boltzmann weight
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*> that is, if I have pmf(i,j) then doing:
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*>
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*>
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*>
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*>
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*> * <pmf ( 1:imax , J)> with the weight of
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*>
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*>
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*>
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*>
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*>
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*> * exp(-beta * pmf( 1:imax , J) )/ integral ( exp(-beta * pmf(
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*> 1:imax , J) ))
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*>
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*>
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*>
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*> and doing this for all the points along y (incrementing j) will give
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*> a pmf for along the y reaction coordinate so I can compare it with
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*> the 1D case of finding the pmf from ABF.
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*>
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*>
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*> I hope I was clear enough please let me know if it's not clear. I'd
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*> appreciate any comment and help on this.
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*>
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*>
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*> Cheers,
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*> Kasra.
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*>
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*>
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**Next message:**Jeffrey Potoff: "Re: Insertion of GPCR in the POPC Bilayer"**Previous message:**Aron Broom: "Re: Insertion of GPCR in the POPC Bilayer"**In reply to:**Kasra Fattah: "Free Energy Calculation Question"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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