Free Energy Calculation Question

From: Kasra Fattah (
Date: Thu Jun 20 2013 - 15:28:28 CDT

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.


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