Tell me more ×
Physics Stack Exchange is a question and answer site for active researchers, academics and students of physics. It's 100% free, no registration required.
up vote 1 down vote favorite

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

share|improve this question
2  
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

1 Answer

up vote 1 down vote accepted

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.

share|improve this answer
well summarized. Thanks. – Chirag Sep 30 '12 at 18:24

Your Answer

 
discard

By posting your answer, you agree to the privacy policy and terms of service.

Not the answer you're looking for? Browse other questions tagged or ask your own question.