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What is theory behind free energy perturbation? Is it way too difficult to understand? Can someone explain it in simple terms.

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Hi Chirag! If you started by saying what you have read on the topic and list what you do (and don't) understand, it would make it much easier for someone to answer at your level… For example, Wikipedia has a very nice page on this topic, so you could read that and come later ask more precise questions… –  F'x Sep 30 '12 at 7:56
Well what exactly I don't understand is... how is it statistically good practice to do forward and backward sampling in simulations based of FEP? PS: I'm not a statistician. –  Chirag Sep 30 '12 at 18:26
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Free energy perturbation is a free energy method, i.e. it allows one to calculate the difference in free energy between two states A and B, during a molecular simulation. Other, and possibly better-known free energy methods, include thermodynamic integration and umbrella sampling.

The idea behind the free energy perturbation method is that, if your states A and B are close enough, i.e. if they represent well-overlapping regions of phase space, you can get information about their free energy difference from one single molecular simulation in one of the states. The big gain of using a small perturbation is that you don't need to actually sample both A and B, because they're close enough.

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well summarized. Thanks. –  Chirag Sep 30 '12 at 18:24
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