**From:** Jerome Henin (*jhenin_at_cmm.chem.upenn.edu*)

**Date:** Sat Apr 26 2008 - 11:30:37 CDT

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Mert,

As you say, no combination of energy values sampled from independent

simulations in states A and B will give you the average in state A

that is needed for FEP.

Instead, to evaluate the FEP average, both energy functions A and B

(or at least their difference) should be computed on-the-fly during a

single simulation in state A. The alchemical free energy feature of

NAMD does just that. Calculation of both potential energy functions is

made possible by providing a "hybrid" topology that describes two

chemical systems at once.

Best,

Jerome

On Sat, Apr 26, 2008 at 6:56 AM, Mert Gür <gurmert_at_gmail.com> wrote:

*> Dear all,
*

*>
*

*> I have a problem understanding the theory of free energy perturbation
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*> method. I have read several papers and have also read the alchemical free
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*> energy perturbation tutorial.
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*>
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*> As explained very simply at this link:
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*>
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*> http://en.wikipedia.org/wiki/Free_energy_perturbation
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*>
*

*> the triangular brackets denote an average over a simulation run for state A.
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*> In practice, one runs a normal simulation for state A, but each time a new
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*> configuration is accepted, the energy for state B is also computed.
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*> Let say I have run a simulation for state A in NAMD and a simulation for
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*> state B in NAMD.
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*> I now have energy values for each snapshot of A and B. So I actually have
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*> the distribution (probability) function for A and B seperately.
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*> If I havent understand it wrong, MD already gives me the Boltzman
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*> distribution so that I have just to take the simple average (sum/N) of any
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*> property I have recorded at N snapshots. By doing so I have the triangular
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*> bracket average.
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*> How do I perform the same for <E(A)-E(B)>A (definition given in the link).
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*> I mean do I simply subtract each energy value I record at each snapshot for
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*> B, from the energy value I recorded for A.
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*> If I do so I dont see how it becomes the average over a simulation run for
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*> state A.
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*>
*

*> Thanks in advance,
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*>
*

*> Mert Gur
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*> Computational Science and Engineering
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*> Koc University
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*> Istanbul/Turkey
*

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