Re: Free Energy Calculation Question

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Jun 20 2013 - 16:18:57 CDT

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 -----
>
> Hi all,
>
>
> I'm calculation the pmf of a system using ABF method. One I did it
> for a 1D collective variable that is the distanceZ of a molecule
> from a specific point along y-direction. Next I'm doing a 2d pmf
> calculation using the collective variable along both x and y
> direction and I get a surface of pmf. Now to test if the results
> from 2d are consistent with my 1d results:
>
>
> Is the following procedure right?
>
>
> I average the results while keeping one of the reaction coordinates
> constant (eg. at a constant y) with respect to the Boltzmann weight
> that is, if I have pmf(i,j) then doing:
>
>
>
>
> * <pmf ( 1:imax , J)> with the weight of
>
>
>
>
>
> * exp(-beta * pmf( 1:imax , J) )/ integral ( exp(-beta * pmf(
> 1:imax , J) ))
>
>
>
> and doing this for all the points along y (incrementing j) will give
> a pmf for along the y reaction coordinate so I can compare it with
> the 1D case of finding the pmf from ABF.
>
>
> I hope I was clear enough please let me know if it's not clear. I'd
> appreciate any comment and help on this.
>
>
> Cheers,
> Kasra.
>
>

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