**From:** Kasra Fattah (*kasra.fattah_at_gmail.com*)

**Date:** Thu Jun 20 2013 - 15:28:28 CDT

**Next message:**Vibhor Agrawal: "Insertion of GPCR in the POPC Bilayer"**Previous message:**Aron Broom: "Re:"**Next in thread:**Aron Broom: "Re: Free Energy Calculation Question"**Reply:**Aron Broom: "Re: Free Energy Calculation Question"**Reply:**Jérôme Hénin: "Re: Free Energy Calculation Question"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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.

**Next message:**Vibhor Agrawal: "Insertion of GPCR in the POPC Bilayer"**Previous message:**Aron Broom: "Re:"**Next in thread:**Aron Broom: "Re: Free Energy Calculation Question"**Reply:**Aron Broom: "Re: Free Energy Calculation Question"**Reply:**Jérôme Hénin: "Re: Free Energy Calculation Question"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Wed Dec 31 2014 - 23:21:19 CST
*