**From:** Mert Gür (*gurmert_at_gmail.com*)

**Date:** Sat Apr 26 2008 - 05:56:26 CDT

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Dear all,

I have a problem understanding the theory of free energy perturbation

method. I have read several papers and have also read the alchemical free

energy perturbation tutorial.

As explained very simply at this link:

http://en.wikipedia.org/wiki/Free_energy_perturbation

the triangular brackets denote an average over a simulation run for state *A

*. In practice, one runs a normal simulation for state *A*, but each time a

new configuration is accepted, the energy for state *B* is also computed.

Let say I have run a simulation for state A in NAMD and a simulation for

state B in NAMD.

I now have energy values for each snapshot of A and B. So I actually have

the distribution (probability) function for A and B seperately.

If I havent understand it wrong, MD already gives me the Boltzman

distribution so that I have just to take the simple average (sum/N) of any

property I have recorded at N snapshots. By doing so I have the triangular

bracket average.

How do I perform the same for <E(A)-E(B)>A (definition given in the link).

I mean do I simply subtract each energy value I record at each snapshot for

B, from the energy value I recorded for A.

If I do so I dont see how it becomes the average over a simulation run for

state *A.*

**

Thanks in advance,

Mert Gur

Computational Science and Engineering

Koc University

Istanbul/Turkey

**Next message:**Jerome Henin: "Re: FEP triangular bracket average"**Previous message:**Alexandre A. Vakhrouchev: "Re: install NAMD on Ubuntu"**Next in thread:**Jerome Henin: "Re: FEP triangular bracket average"**Reply:**Jerome Henin: "Re: FEP triangular bracket average"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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